Add autoupdate command

docs/autoupdate.rst

@@ -13,17 +13,17 @@ Planemo provides a ``autoupdate`` subcommand which can be used to perform this t
 There are various flags which can be applied; these are some of the most important:
   - ``--recursive``, which performs the autoupdate recursively on subdirectories
   - ``--dry-run``, which checks if tool requirements are up-to-date without making the necessary change automatically
-  - ``--test``, which runs tests on all autoupdated tools
+  - ``--test``, which runs tests on all autoupdated tools. If this flag is used, all options available for ``planemo test`` are also available.
   - ``--update_test_data`` (if ``--test`` is also selected) which will update test data for failed tests
+  - ``--skiplist``, pointing to a list of tool wrappers for which updates should be skipped
+  - ``--skip_requirements`` with a comma-separated list of packages not to update.  ``python``, ``perl``, ``r-base`` are skipped by default.
 
-One of the most efficient ways to use it is by implementing a CI cron job which runs the command on an entire GitHub repository of tools.
+One of the most efficient ways to use it is by implementing a CI cron job which runs the command on an entire GitHub repository of tool wrappers.
 
 Formatting tools
 =============================
 
- ``autoupdate`` assumes that XML tools are formatted in a certain way - in accordance with the `IUC best practices`_
-
-<https://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_xml.html/>`__. In particular:
+``autoupdate`` assumes that XML tools are formatted in a certain way - in accordance with the `IUC best practices`_. In particular:
 
   - the tool ``version`` attribute must be set to ``@TOOL_VERSION@+galaxy0`` or ``@TOOL_VERSION@+galaxy@GALAXY_VERSION``
   - A token ``@TOOL_VERSION@`` should be created which corresponds to the version number of the main requirement.
@@ -33,8 +33,8 @@ Formatting tools
 Implementing an autoupdate CI job
 =================================
 
-  A useful way to use the autoupdate command is to implement it as a CI job, so that tools in a repo can be updated on a regular basis (e.g. weekly). An example implementation is the `planemo-autoupdate`_ GitHub bot.
+ A useful way to use the autoupdate command is to implement it as a CI job, so that tools in a repo can be updated on a regular basis (e.g. weekly). An example implementation is the `planemo-autoupdate`_ GitHub bot.
 
-<https://github.com/planemo-autoupdate/autoupdate/>`__
 
 .. _IUC best practices: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html
+.. _planemo-autoupdate: https://github.com/planemo-autoupdate/autoupdate

docs/commands.rst

@@ -7,6 +7,7 @@ implemented as a subcommand of the ``planemo`` executable. This section of the
 documentation describes these commands.
 
 
+.. include:: commands/autoupdate.rst
 .. include:: commands/ci_find_repos.rst
 .. include:: commands/ci_find_tools.rst
 .. include:: commands/clone.rst

docs/commands/autoupdate.rst

@@ -26,6 +26,10 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
       --skiplist TEXT                 Skiplist file, containing a list of tools for
                                       which autoupdate should be skipped.
 
+      --skip_requirements TEXT        Comma-separated list of requirements which
+                                      should be not be updated. Default is
+                                      python,r-base,perl.
+
       --update_test_data              Update test-data directory with job outputs
                                       (normally written to directory
                                       --job_output_files if specified.)
@@ -52,6 +56,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
       --test_output_junit PATH        Output test report (jUnit style - for CI
                                       systems
 
+      --test_output_allure DIRECTORY  Output test allure2 framework resutls
       --test_output_json PATH         Output test report (planemo json) defaults to
                                       tool_test_output.json.
 
@@ -64,7 +69,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
       --galaxy_root DIRECTORY         Root of development galaxy directory to
                                       execute command with.
 
-      --galaxy_python_version [3|3.5|3.6|3.7|3.8]
+      --galaxy_python_version [3|3.6|3.7|3.8|3.9]
                                       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

docs/planemo.commands.rst

@@ -4,6 +4,14 @@ planemo.commands package
 Submodules
 ----------
 
+planemo.commands.cmd\_autoupdate module
+---------------------------------------
+
+.. automodule:: planemo.commands.cmd_autoupdate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 planemo.commands.cmd\_ci\_find\_repos module
 --------------------------------------------
 

docs/planemo.engine.rst

@@ -4,6 +4,14 @@ planemo.engine package
 Submodules
 ----------
 
+planemo.engine.autoupdate module
+--------------------------------
+
+.. automodule:: planemo.engine.autoupdate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 planemo.engine.cwltool module
 -----------------------------
 

planemo/autoupdate.py

@@ -54,9 +54,6 @@ def check_conda(tool_name, ctx, **kwds):
         error("Conda is not installed! Try running planemo conda_init.")
     target = planemo.conda.conda_util.CondaTarget(tool_name)
     search_results = conda_util.best_search_result(target, conda_context=conda_context)
-    # if search_results[0]['version'] == tool_version:
-    #     return None
-    # else:
     return search_results[0]['version']
 
 
@@ -144,7 +141,6 @@ def perform_required_update(ctx, xml_files, tool_path, requirements, tokens, xml
             if wrapper_version_token in v:
                 xml_to_update[k].append({'type': 'token', 'tag': v[wrapper_version_token]['tag'], 'value': 0})
 
-    # print(xml_to_update)
     # finally, update each file separately
     for k, v in xml_files.items():
         update_xml(k, v, xml_to_update[k], wrapper_version_token, is_macro=(k != tool_path))
@@ -153,7 +149,7 @@ def perform_required_update(ctx, xml_files, tool_path, requirements, tokens, xml
     return set(xml_files)
 
 
-def autoupdate(ctx, tool_path, modified_files=set(), **kwds):
+def autoupdate_tool(ctx, tool_path, modified_files=set(), **kwds):
     """
     Autoupdate an XML file
     """

planemo/commands/cmd_autoupdate.py

@@ -68,13 +68,13 @@ def skip_requirements_option():
 @options.recursive_option()
 @test_option()
 @skiplist_option()
+@skip_requirements_option()
 @options.test_options()
 @options.galaxy_target_options()
 @options.galaxy_config_options()
 @options.report_level_option()
 @options.report_xunit()
 @options.fail_level_option()
-@options.skip_option()
 @command_function
 def cli(ctx, paths, **kwds):
     """Auto-update tool requirements by checking against Conda and updating if newer versions are available."""
@@ -89,7 +89,7 @@ def cli(ctx, paths, **kwds):
             continue
         info("Auto-updating tool %s" % tool_path)
         try:
-            updated = autoupdate.autoupdate(ctx, tool_path, modified_files=modified_files, **kwds)
+            updated = autoupdate.autoupdate_tool(ctx, tool_path, modified_files=modified_files, **kwds)
             if updated:
                 modified_files.update(updated)
         except Exception as e:
@@ -106,14 +106,13 @@ def cli(ctx, paths, **kwds):
         else:
             with temp_directory(dir=ctx.planemo_directory) as temp_path:
                 # only test tools in updated directories
-                modified_paths = [tool_path for tool_path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive) if tool_path in modified_files]
+                modified_paths = [path for path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive) if path in modified_files]
                 info(f"Running tests for the following auto-updated tools: {', '.join(modified_paths)}")
                 runnables = for_paths(modified_paths, temp_path=temp_path)
                 kwds["engine"] = "galaxy"
                 return_value = test_runnables(ctx, runnables, original_paths=paths, **kwds)
-
+                exit_codes.append(return_value)
     return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
-    ctx.exit(return_value)
 
 
 def handle_tool_load_error(tool_path, tool_xml):