If virtualenv not on PATH, have Planemo create one for Galaxy.

jmchilton · jmchilton · commit 5b97f2e3c50b · 2015-11-20T11:29:41.000Z
http://dev.list.galaxyproject.org/Planemo-0-20-0-and-xunit-td4668334.html $ cd project_templates/demo $ which virtualenv virtualenv not found $ ../../.venv/bin/planemo s cat.xml git --git-dir /home/john/.planemo/gx_repo fetch >/dev/null 2>&1 cd /tmp/tmpfBhxgp; git clone --branch 'dev' '/home/john/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/john/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/john/workspace/planemo/.venv/bin/planemo virtualenv $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} Cloning into 'galaxy-dev'... done. Using real prefix '/usr' New python executable in /home/john/.planemo/gx_venv/bin/python Installing setuptools, pip, wheel...done. Set COMMON_STARTUP_ARGS to --skip-venv --dev-wheels ....
diff --git a/planemo/commands/cmd_virtualenv.py b/planemo/commands/cmd_virtualenv.py
@@ -0,0 +1,24 @@
+import click
+
+from planemo.cli import pass_context
+from planemo import virtualenv
+
+VIRTUALENV_PATH_TYPE = click.Path(
+    exists=False,
+    writable=True,
+    resolve_path=True,
+)
+
+
+@click.command("virtualenv")
+@click.argument("virtualenv_path",
+                metavar="VIRTUALENV_PATH",
+                type=VIRTUALENV_PATH_TYPE)
+@pass_context
+def cli(ctx, virtualenv_path):
+    """Create a virtualenv.
+
+    Use virtualenv as library to create a virtualenv for Galaxy if virtualenv
+    is not available on the PATH.
+    """
+    virtualenv.create_and_exit(virtualenv_path)
diff --git a/planemo/galaxy_run.py b/planemo/galaxy_run.py
@@ -2,17 +2,15 @@
 import string
 
 from planemo.io import info, shell_join
+from planemo.virtualenv import create_command
 from galaxy.tools.deps.commands import shell
 
 
 # Activate galaxy's virtualenv if present (needed for tests say but not for
 # server because run.sh does this).
 ACTIVATE_COMMAND = "[ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate"
-CREATE_COMMAND = shell_join(
-    'if [ ! -e $GALAXY_VIRTUAL_ENV ]',
-    ' then type virtualenv >/dev/null 2>&1 && virtualenv $GALAXY_VIRTUAL_ENV',
-    ' else echo "Reusing existing virtualenv $GALAXY_VIRTUAL_ENV"',
-    ' fi',
+CREATE_COMMAND_TEMPLATE = string.Template(
+    'if [ ! -e $GALAXY_VIRTUAL_ENV ]; then $create_virtualenv; fi',
 )
 PRINT_VENV_COMMAND = shell_join(
     'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
@@ -35,10 +33,13 @@
 
 
 def setup_venv(ctx, kwds):
+    create_template_params = {
+        'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV")
+    }
     return shell_join(
         locate_galaxy_virtualenv(ctx, kwds),
         PRINT_VENV_COMMAND if ctx.verbose else None,
-        CREATE_COMMAND,
+        CREATE_COMMAND_TEMPLATE.safe_substitute(create_template_params),
         PRINT_VENV_COMMAND if ctx.verbose else None,
         ACTIVATE_COMMAND,
     )
diff --git a/planemo/virtualenv.py b/planemo/virtualenv.py
@@ -0,0 +1,26 @@
+""" Utilities for using virtualenv as library and planemo command.
+"""
+from __future__ import absolute_import
+
+import os
+import sys
+
+import virtualenv
+from galaxy.tools.deps.commands import which
+
+
+def create_and_exit(virtualenv_path):
+    sys.argv = ["virtualenv", virtualenv_path]
+    return virtualenv.main()
+
+
+def create_command(virtualenv_path):
+    """ If virtualenv is on Planemo's path use it, otherwise use the planemo
+    subcommand virtualenv to create the virtualenv.
+    """
+    planemo_path = os.path.abspath(sys.argv[0])
+    virtualenv_on_path = which("virtualenv")
+    if virtualenv_on_path:
+        return " ".join([os.path.abspath(virtualenv_on_path), virtualenv_path])
+    else:
+        return " ".join([planemo_path, "virtualenv", virtualenv_path])
diff --git a/requirements.txt b/requirements.txt
@@ -6,3 +6,4 @@ docutils
 jinja2
 glob2
 cwltool
+virtualenv
diff --git a/setup.py b/setup.py
@@ -23,6 +23,7 @@
     'PyGithub',
     'bioblend',
     'glob2',
+    'virtualenv',
 ]
 
 # Only import cwltool for Python 2.7.

-Original file line number
+Diff line change
 jinja2
 glob2
 cwltool
 +virtualenv
Original file line number	Diff line number	Diff line change
`@@ -23,6 +23,7 @@`
`23`	`23`	`'PyGithub',`
`24`	`24`	`'bioblend',`
`25`	`25`	`'glob2',`
	`26`	`+ 'virtualenv',`
`26`	`27`	`]`
`27`	`28`
`28`	`29`	`# Only import cwltool for Python 2.7.`