Depend on new galaxy-lib on PyPI instead of planemo_ext hacks...

galaxyproject · Dec 20, 2015 · 1f13855 · 1f13855
1 parent 3a42d71
commit 1f13855
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Showing 112 changed files with 8 additions and 15,342 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -2,5 +2,5 @@
 	path = planemo/xml/xsd/tool
 	url = https://github.com/JeanFred/Galaxy-XSD
 [submodule "planemo_ext/cwl2script"]
-	path = planemo_ext/cwl2script
+	path = planemo/cwl/cwl2script
 	url = https://github.com/common-workflow-language/cwl2script.git
diff --git a/planemo/cli.py b/planemo/cli.py
@@ -4,15 +4,9 @@
 
 import click
 
-# Hack to place Galaxy modules on PYTHONPATH - without
-# actually having them on the real external PYTHONPATH.
-import planemo_ext
-planemo_ext_path = planemo_ext.__path__[0]
-sys.path.append(os.path.join(planemo_ext_path))
-
-from .io import error  # noqa, import must happen after Galaxy hack
-from .config import read_global_config  # noqa, ditto
-from planemo import __version__  # noqa, ditto
+from .io import error
+from .config import read_global_config
+from planemo import __version__
 
 PYTHON_2_7_COMMANDS = ["cwl_run", "cwl_script"]
 IS_PYTHON_2_7 = sys.version_info[0] == 2 and sys.version_info[1] >= 7

diff --git a/planemo_ext/cwl2script → planemo/cwl/cwl2script b/planemo_ext/cwl2script → planemo/cwl/cwl2script
diff --git a/planemo/cwl/script.py b/planemo/cwl/script.py
@@ -23,7 +23,7 @@
     process = None
 
 try:
-    from cwl2script import cwl2script
+    from .cwl2script import cwl2script
 except ImportError:
     cwl2script = None
 

diff --git a/planemo_ext/galaxy/__init__.py b/planemo_ext/galaxy/__init__.py
diff --git a/planemo_ext/galaxy/eggs/__init__.py b/planemo_ext/galaxy/eggs/__init__.py
diff --git a/planemo_ext/galaxy/exceptions.py b/planemo_ext/galaxy/exceptions.py
diff --git a/planemo_ext/galaxy/jobs/__init__.py b/planemo_ext/galaxy/jobs/__init__.py
diff --git a/planemo_ext/galaxy/jobs/metrics/__init__.py b/planemo_ext/galaxy/jobs/metrics/__init__.py
diff --git a/planemo_ext/galaxy/jobs/metrics/collectl/__init__.py b/planemo_ext/galaxy/jobs/metrics/collectl/__init__.py
diff --git a/planemo_ext/galaxy/jobs/metrics/collectl/cli.py b/planemo_ext/galaxy/jobs/metrics/collectl/cli.py