Refactor galaxy modules ....

 - planemo.galaxy_test -> planemo.galaxy.test
 - planemo.galaxy_config -> planemo.galaxy.config
 - planemo.galaxy_run -> planemo.galaxy.run
 - planemo.galaxy_serve -> planemo.galaxy.serve

Author: jmchilton

docs/planemo.galaxy.rst

@@ -0,0 +1,53 @@
+planemo.galaxy package
+======================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    planemo.galaxy.test
+
+Submodules
+----------
+
+planemo.galaxy.config module
+----------------------------
+
+.. automodule:: planemo.galaxy.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+planemo.galaxy.profiles module
+------------------------------
+
+.. automodule:: planemo.galaxy.profiles
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+planemo.galaxy.run module
+-------------------------
+
+.. automodule:: planemo.galaxy.run
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+planemo.galaxy.serve module
+---------------------------
+
+.. automodule:: planemo.galaxy.serve
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: planemo.galaxy
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/planemo.galaxy_test.rst renamed to docs/planemo.galaxy.test.rst

@@ -1,21 +1,21 @@
-planemo.galaxy_test package
+planemo.galaxy.test package
 ===========================
 
 Submodules
 ----------
 
-planemo.galaxy_test.actions module
+planemo.galaxy.test.actions module
 ----------------------------------
 
-.. automodule:: planemo.galaxy_test.actions
+.. automodule:: planemo.galaxy.test.actions
     :members:
     :undoc-members:
     :show-inheritance:
 
-planemo.galaxy_test.structures module
+planemo.galaxy.test.structures module
 -------------------------------------
 
-.. automodule:: planemo.galaxy_test.structures
+.. automodule:: planemo.galaxy.test.structures
     :members:
     :undoc-members:
     :show-inheritance:
@@ -24,7 +24,7 @@ planemo.galaxy_test.structures module
 Module contents
 ---------------
 
-.. automodule:: planemo.galaxy_test
+.. automodule:: planemo.galaxy.test
     :members:
     :undoc-members:
     :show-inheritance:

docs/planemo.rst

@@ -8,7 +8,7 @@ Subpackages
 
     planemo.commands
     planemo.cwl
-    planemo.galaxy_test
+    planemo.galaxy
     planemo.linters
     planemo.reports
     planemo.shed
@@ -58,30 +58,6 @@ planemo.exit_codes module
     :undoc-members:
     :show-inheritance:
 
-planemo.galaxy_config module
-----------------------------
-
-.. automodule:: planemo.galaxy_config
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-planemo.galaxy_run module
--------------------------
-
-.. automodule:: planemo.galaxy_run
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-planemo.galaxy_serve module
----------------------------
-
-.. automodule:: planemo.galaxy_serve
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 planemo.git module
 ------------------
 

planemo/commands/cmd_serve.py

@@ -1,7 +1,7 @@
 import click
 
 from planemo.cli import pass_context
-from planemo import galaxy_serve
+from planemo.galaxy import galaxy_serve
 from planemo import options
 
 
@@ -34,4 +34,4 @@ def cli(ctx, paths, **kwds):
     proof yet so please careful and do not try this against production Galaxy
     instances.
     """
-    galaxy_serve.serve(ctx, paths, **kwds)
+    galaxy_serve(ctx, paths, **kwds)

planemo/commands/cmd_shed_serve.py

@@ -5,7 +5,7 @@
 
 from planemo.cli import pass_context
 from planemo import options
-from planemo import galaxy_serve
+from planemo.galaxy import shed_serve
 from planemo import shed
 from planemo import io
 
@@ -29,7 +29,7 @@ def cli(ctx, paths, **kwds):
     logged into and explored interactively.
     """
     install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
-    with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
+    with shed_serve(ctx, install_args_list, **kwds) as config:
         gx_url = "http://localhost:%d/" % config.port
         io.info("Galaxy running with tools installed at %s" % gx_url)
         time.sleep(1000000)

planemo/commands/cmd_shed_test.py

@@ -7,9 +7,9 @@
 
 from planemo.cli import pass_context
 from planemo import options
-from planemo import galaxy_serve
+from planemo.galaxy.serve import shed_serve
 from planemo import shed
-from planemo import galaxy_test
+from planemo.galaxy.test import run_in_config
 
 
 @click.command("shed_test")
@@ -36,9 +36,9 @@ def cli(ctx, paths, **kwds):
     port = get_free_port()
     kwds["port"] = port
     return_code = 1
-    with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
+    with shed_serve(ctx, install_args_list, **kwds) as config:
         config.kill()
-        return_code = galaxy_test.run_in_config(
+        return_code = run_in_config(
             ctx,
             config,
             installed=True,

planemo/commands/cmd_test.py

@@ -4,9 +4,9 @@
 
 from planemo.cli import pass_context
 from planemo import options
-from planemo import galaxy_config
+from planemo.galaxy import galaxy_config
 
-from planemo.galaxy_test import (
+from planemo.galaxy.test import (
     run_in_config,
 )
 
@@ -55,7 +55,7 @@ def cli(ctx, paths, **kwds):
     please careful and do not try this against production Galaxy instances.
     """
     kwds["for_tests"] = True
-    with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
+    with galaxy_config(ctx, paths, **kwds) as config:
         return_value = run_in_config(ctx, config, **kwds)
         if return_value:
             sys.exit(return_value)

planemo/commands/cmd_test_reports.py

@@ -5,7 +5,7 @@
 from planemo.cli import pass_context
 from planemo import io
 from planemo import options
-from planemo.galaxy_test import StructuredData, handle_reports
+from planemo.galaxy.test import StructuredData, handle_reports
 
 
 @click.command('test_reports')

planemo/commands/cmd_tool_factory.py

@@ -3,7 +3,7 @@
 import click
 from planemo.cli import pass_context
 from planemo import options
-from planemo import galaxy_serve
+from planemo.galaxy import serve
 
 
 @click.command('tool_factory')
@@ -19,4 +19,4 @@ def cli(ctx, **kwds):
     """
     mod_dir = os.path.dirname(__file__)
     tf_dir = os.path.join(mod_dir, '..', '..', 'planemo_ext', 'tool_factory_2')
-    galaxy_serve.serve(ctx, [os.path.abspath(tf_dir)], **kwds)
+    serve(ctx, [os.path.abspath(tf_dir)], **kwds)

planemo/conda.py

@@ -1,6 +1,7 @@
 """ Planemo specific utilities for dealing with conda, extending Galaxy's
 features with planemo specific idioms.
 """
+from __future__ import absolute_import
 
 from galaxy.tools.deps import conda_util
 from planemo.io import shell

planemo/cwl/run.py

@@ -1,5 +1,5 @@
 from planemo.io import conditionally_captured_io
-from planemo import galaxy_serve
+from planemo.galaxy.serve import serve_daemon
 from .client import run_cwl_tool
 from planemo import io
 
@@ -15,7 +15,7 @@ def run_galaxy(ctx, path, job_path, **kwds):
     kwds["cwl"] = True
     conformance_test = kwds.get("conformance_test", False)
     with conditionally_captured_io(conformance_test):
-        with galaxy_serve.serve_daemon(ctx, [path], **kwds) as config:
+        with serve_daemon(ctx, [path], **kwds) as config:
             try:
                 cwl_run = run_cwl_tool(path, job_path, config, **kwds)
             except Exception:

planemo/galaxy/__init__.py

@@ -0,0 +1,19 @@
+"""Entry-point for Galaxy specific functionality in Planemo."""
+
+from __future__ import absolute_import
+
+from .config import galaxy_config
+from .run import (
+    setup_venv,
+    run_galaxy_command,
+)
+from .serve import shed_serve
+from .serve import serve as galaxy_serve
+
+__all__ = [
+    "galaxy_config",
+    "setup_venv",
+    "run_galaxy_command",
+    "galaxy_serve",
+    "shed_serve",
+]

planemo/galaxy_config.py renamed to planemo/galaxy/config.py

@@ -13,7 +13,11 @@
 
 import click
 
-from planemo import galaxy_run
+from .run import (
+    setup_common_startup_args,
+    setup_venv,
+    DOWNLOAD_GALAXY,
+)
 from planemo.conda import build_conda_context
 from planemo.io import warn
 from planemo.io import shell
@@ -547,7 +551,7 @@ def _install_galaxy(ctx, config_directory, env, kwds):
 def _install_galaxy_via_download(ctx, config_directory, env, kwds):
     branch = _galaxy_branch(kwds)
     tar_cmd = "tar -zxvf %s" % branch
-    command = galaxy_run.DOWNLOAD_GALAXY + "; %s | tail" % tar_cmd
+    command = DOWNLOAD_GALAXY + "; %s | tail" % tar_cmd
     _install_with_command(ctx, config_directory, command, env, kwds)
 
 
@@ -599,14 +603,14 @@ def _install_with_command(ctx, config_directory, command, env, kwds):
         pip_install_command = PIP_INSTALL_CMD % " ".join(pip_installs)
     else:
         pip_install_command = ""
-    setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
+    setup_venv_command = setup_venv(ctx, kwds)
     install_cmd = shell_join(
         "cd %s" % config_directory,
         command,
         "cd galaxy-dev",
         setup_venv_command,
         pip_install_command,
-        galaxy_run.setup_common_startup_args(),
+        setup_common_startup_args(),
         COMMAND_STARTUP_COMMAND,
     )
     shell(install_cmd, env=env)

planemo/galaxy_run.py renamed to planemo/galaxy/run.py

@@ -97,3 +97,10 @@ def run_galaxy_command(ctx, command, env, action, daemon=False):
         ctx.vlog('%s="%s"' % (key, value))
     ctx.vlog("============================")
     return shell(command, env=env)
+
+__all__ = [
+    "setup_venv",
+    "run_galaxy_command",
+    "DOWNLOAD_GALAXY",
+    "setup_common_startup_args",
+]

planemo/galaxy_serve.py renamed to planemo/galaxy/serve.py

@@ -1,8 +1,11 @@
 import contextlib
 import os
 
-from planemo import galaxy_config
-from planemo import galaxy_run
+from .config import galaxy_config
+from .run import (
+    setup_venv,
+    run_galaxy_command,
+)
 from planemo import io
 
 
@@ -15,9 +18,9 @@ def serve(ctx, paths, **kwds):
     if daemon:
         kwds["no_cleanup"] = True
 
-    with galaxy_config.galaxy_config(ctx, paths, **kwds) as config:
+    with galaxy_config(ctx, paths, **kwds) as config:
         # TODO: Allow running dockerized Galaxy here instead.
-        setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
+        setup_venv_command = setup_venv(ctx, kwds)
         run_script = os.path.join(config.galaxy_root, "run.sh")
         run_script += " $COMMON_STARTUP_ARGS"
         if daemon:
@@ -34,7 +37,7 @@ def serve(ctx, paths, **kwds):
             run_script,
         )
         action = "Starting galaxy"
-        galaxy_run.run_galaxy_command(
+        run_galaxy_command(
             ctx,
             cmd,
             config.env,

planemo/galaxy_test/__init__.py renamed to planemo/galaxy/test/__init__.py

@@ -4,7 +4,10 @@
 
 from . import structures as test_structures
 from planemo.io import info, warn, shell_join
-from planemo import galaxy_run
+from planemo.galaxy.run import (
+    run_galaxy_command,
+    setup_venv,
+)
 from planemo.reports import build_report
 
 
@@ -58,15 +61,15 @@ def run_in_config(ctx, config, **kwds):
             'export COMMON_STARTUP_ARGS; '
             'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"'
         )
-    setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
+    setup_venv_command = setup_venv(ctx, kwds)
     cmd = shell_join(
         cd_to_galaxy_command,
         setup_common_startup_args,
         setup_venv_command,
         test_cmd,
     )
     action = "Testing tools"
-    return_code = galaxy_run.run_galaxy_command(
+    return_code = run_galaxy_command(
         ctx,
         cmd,
         config.env,

planemo/galaxy_test/actions.py renamed to planemo/galaxy/test/actions.py

@@ -1,6 +1,8 @@
 """ Click definitions for various shared options and arguments.
 """
 
+from __future__ import absolute_import
+
 import functools
 import os