Tool shed publishing support.

 - New shed_upload command that can tar up a repository and publish it to various tool sheds.
 - Introduce global config file ~/.planemo.yml with optional tool sheds API keys, tool shed username, etc...
 - New config_init command to setup a template for this global config file.
 - Allow each repo to contain an optional .shed.yml describing name of repository (will fill this out with more options).

Have to disable Python 3.4 support because bioblend doesn't support Python 3.4.

Warning: This depends on very new tool shed features that have not even been merged into galaxy-central yet.

.travis.yml

@@ -3,7 +3,7 @@
 language: python
 
 python:
-  - "3.4"
+#  - "3.4"
   - "2.7"
   - "2.6"
   - "pypy"

docs/commands.rst

@@ -10,11 +10,13 @@ documentation describes these commands.
 .. include:: commands/brew.rst
 .. include:: commands/brew_env.rst
 .. include:: commands/brew_init.rst
+.. include:: commands/config_init.rst
 .. include:: commands/docker_build.rst
 .. include:: commands/docker_shell.rst
 .. include:: commands/lint.rst
 .. include:: commands/project_init.rst
 .. include:: commands/serve.rst
+.. include:: commands/shed_upload.rst
 .. include:: commands/syntax.rst
 .. include:: commands/test.rst
 .. include:: commands/tool_init.rst

docs/commands/config_init.rst

@@ -0,0 +1,22 @@
+
+``config_init`` command
+===============================
+
+This section is auto-generated from the help text for the planemo command
+``config_init``. This help message can be generated with ``planemo config_init
+--help``.
+
+**Usage**::
+
+    planemo config_init [OPTIONS] PROJECT
+
+**Help**
+
+Help initialize global configuration (in home directory) for Planemo.
+
+**Options**::
+
+
+      --template TEXT
+      --help           Show this message and exit.
+    

docs/commands/shed_upload.rst

@@ -0,0 +1,31 @@
+
+``shed_upload`` command
+===============================
+
+This section is auto-generated from the help text for the planemo command
+``shed_upload``. This help message can be generated with ``planemo shed_upload
+--help``.
+
+**Usage**::
+
+    planemo shed_upload [OPTIONS] PROJECT
+
+**Help**
+
+Upload a tool directory as a tarball to a tool shed.
+
+**Options**::
+
+
+      --message TEXT        Commit message for tool shed upload.
+      --owner TEXT          Tool shed repository owner (username).
+      --name TEXT           Repository name (default to tool directory name).
+      --shed_target TEXT    Tool shed to target (toolshed/testtoolshed/local/url).
+      --shed_key TEXT       API key for shed access (required unless e-mail/pass
+                            specified).
+      --shed_email TEXT     E-mail for shed auth (required unless shed_key is
+                            specified).
+      --shed_password TEXT  Password for shed auth (required unless shed_key is
+                            specified).
+      --help                Show this message and exit.
+    

docs/planemo.rst

@@ -19,6 +19,14 @@ planemo.cli module
     :undoc-members:
     :show-inheritance:
 
+planemo.config module
+---------------------
+
+.. automodule:: planemo.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 planemo.galaxy_config module
 ----------------------------
 
@@ -51,6 +59,14 @@ planemo.options module
     :undoc-members:
     :show-inheritance:
 
+planemo.shed module
+-------------------
+
+.. automodule:: planemo.shed
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

planemo/cli.py

@@ -2,6 +2,8 @@
 import sys
 import click
 from .io import error
+from .config import read_global_config
+
 
 CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
 COMMAND_ALIASES = {
@@ -16,6 +18,13 @@ class Context(object):
     def __init__(self):
         self.verbose = False
         self.home = os.getcwd()
+        self._global_config = None
+
+    @property
+    def global_config(self):
+        if self._global_config is None:
+            self._global_config = read_global_config()
+        return self._global_config
 
     def log(self, msg, *args):
         """Logs a message to stderr."""

planemo/commands/cmd_config_init.py

@@ -0,0 +1,59 @@
+"""
+"""
+import os
+
+import click
+
+from planemo.cli import pass_context
+from planemo import options
+from planemo import config
+from planemo.io import warn, info
+
+CONFIG_TEMPLATE = """## Planemo Global Configuration File.
+## Everything in this file is completely optional - these values can all be
+## configured via command line options for the corresponding commands.
+
+## Specify a default galaxy_root for test and server commands here.
+#galaxy_root: /path/to/galaxy_root
+## Username used with toolshed(s).
+#shed_username: "<TODO>"
+sheds:
+  # For each tool shed you wish to target, uncomment key or both email and
+  # password.
+  toolshed:
+    #key: "<TODO>"
+    #email: "<TODO>"
+    #password: "<TODO>"
+  testtoolshed
+    #key: "<TODO>"
+    #email: "<TODO>"
+    #password: "<TODO>"
+  local
+    #key: "<TODO>"
+    #email: "<TODO>"
+    #password: "<TODO>"
+"""
+SUCCESS_MESSAGE = (
+    "Wrote configuration template to %s, "
+    "please open with editor and fill out."
+)
+
+
+@click.command("config_init")
+@options.optional_project_arg(exists=None)
+@click.option(
+    '--template',
+    default=None
+)
+@pass_context
+def cli(ctx, path, template=None, **kwds):
+    """Help initialize global configuration (in home directory) for Planemo.
+    """
+    # TODO: prompt for values someday.
+    config_path = config.global_config_path()
+    if os.path.exists(config_path):
+        warn("File %s already exists, exiting." % config_path)
+        return -1
+    with open(config_path, "w") as f:
+        f.write(CONFIG_TEMPLATE)
+        info(SUCCESS_MESSAGE % config_path)

planemo/commands/cmd_shed_upload.py

@@ -0,0 +1,70 @@
+"""
+"""
+import click
+
+from planemo.cli import pass_context
+from planemo import options
+from planemo import shed
+from planemo.io import error
+from planemo.io import info
+from planemo.io import shell
+
+
+# TODO: Implement alternative tool per repo upload strategy.
+# TODO: Use git commit hash and origin to generated commit message.
+@click.command("shed_upload")
+@options.optional_project_arg(exists=True)
+@click.option(
+    '--message',
+    help="Commit message for tool shed upload."
+)
+@click.option(
+    '--owner',
+    help="Tool shed repository owner (username)."
+)
+@click.option(
+    '--name',
+    help="Repository name (default to tool directory name)."
+)
+@click.option(
+    '--shed_target',
+    help="Tool shed to target (toolshed/testtoolshed/local/url).",
+    default="toolshed",
+)
+@click.option(
+    '--shed_key',
+    help="API key for shed access (required unless e-mail/pass specified)."
+)
+@click.option(
+    '--shed_email',
+    help="E-mail for shed auth (required unless shed_key is specified)."
+)
+@click.option(
+    '--shed_password',
+    help="Password for shed auth (required unless shed_key is specified)."
+)
+@click.option(
+    '--tar_only',
+    is_flag=True,
+    help="Produce tar file for upload but do not publish to a tool shed.",
+)
+@pass_context
+def cli(ctx, path, template=None, **kwds):
+    """Upload a tool directory as a tarball to a tool shed.
+    """
+    tar_path = shed.build_tarball(path)
+    if kwds["tar_only"]:
+        shell("cp %s shed_upload.tar.gz" % tar_path)
+        return 0
+    tsi = shed.tool_shed_client(ctx, **kwds)
+    update_kwds = {}
+    message = kwds.get("message", None)
+    if message:
+        update_kwds["commit_message"] = message
+    repo_id = shed.find_repository_id(ctx, tsi, path, **kwds)
+    try:
+        tsi.repositories.update_repository(repo_id, tar_path, **update_kwds)
+    except Exception as e:
+        error(e.read())
+        return -1
+    info("Repository updated successfully.")

planemo/config.py

@@ -0,0 +1,23 @@
+import os
+import yaml
+
+DEFAULT_CONFIG = {
+}
+
+
+def global_config_path():
+    config_path = os.environ.get(
+        "PLANEMO_GLOBAL_CONFIG_PATH",
+        "~/.planemo.yml"
+    )
+    config_path = os.path.expanduser(config_path)
+    return config_path
+
+
+def read_global_config():
+    config_path = global_config_path()
+    if not os.path.exists(config_path):
+        return DEFAULT_CONFIG
+
+    with open(config_path) as f:
+        return yaml.load(f)

planemo/shed.py

@@ -0,0 +1,109 @@
+import os
+from tempfile import mkstemp
+import tarfile
+import yaml
+try:
+    from bioblend import toolshed
+except ImportError:
+    toolshed = None
+
+
+# Planemo generated or consumed files that do not need to be uploaded to the
+# tool shed.
+PLANEMO_FILES = [
+    "tool_test_output.html",
+    ".travis",
+    ".travis.yml",
+    ".shed.yml"
+]
+SHED_SHORT_NAMES = {
+    "toolshed": "https://toolshed.g2.bx.psu.edu/",
+    "testtoolshed": "https://testtoolshed.g2.bx.psu.edu/",
+    "local": "http://localhost:9009/"
+}
+
+
+def shed_repo_config(path):
+    shed_yaml_path = os.path.join(path, ".shed.yml")
+    if os.path.exists(shed_yaml_path):
+        with open(shed_yaml_path, "r") as f:
+            return yaml.load(f)
+    else:
+        return {}
+
+
+def tool_shed_client(ctx, **kwds):
+    shed_target = kwds.get("shed_target")
+    global_config = ctx.global_config
+    if global_config and "sheds" in global_config:
+        sheds_config = global_config["sheds"]
+        shed_config = sheds_config.get(shed_target, {})
+    else:
+        shed_config = {}
+
+    def prop(key):
+        return kwds.get("shed_%s" % key, None) or shed_config.get(key, None)
+
+    url = _tool_shed_url(kwds)
+    key = prop("key")
+    email = prop("email")
+    password = prop("password")
+    tsi = toolshed.ToolShedInstance(
+        url=url,
+        key=key,
+        email=email,
+        password=password
+    )
+    return tsi
+
+
+def find_repository_id(ctx, tsi, path, **kwds):
+    repo_config = shed_repo_config(path)
+    owner = kwds.get("owner", None) or repo_config.get("owner", None)
+    name = kwds.get("name", None) or repo_config.get("name", None)
+    if owner is None:
+        owner = ctx.global_config.get("shed_username", None)
+    if name is None:
+        name = os.path.basename(os.path.abspath(path))
+    repos = tsi.repositories.get_repositories()
+
+    def matches(r):
+        return r["owner"] == owner and r["name"] == name
+
+    matching_repos = filter(matches, repos)
+    if not matching_repos:
+        message = "Failed to find repository for owner/name %s/%s"
+        raise Exception(message % (owner, name))
+    repo_id = matching_repos[0]["id"]
+    return repo_id
+
+
+def build_tarball(tool_path):
+    """Build a tool-shed tar ball for the specified path, caller is
+    responsible for deleting this file.
+    """
+    fd, temp_path = mkstemp()
+    try:
+        with tarfile.open(temp_path, "w:gz") as tar:
+            for name in os.listdir(tool_path):
+                path = os.path.join(tool_path, name)
+                tar.add(path, name, recursive=True, exclude=_tar_excludes)
+    finally:
+        os.close(fd)
+    return temp_path
+
+
+def _tool_shed_url(kwds):
+    url = kwds.get("shed_target")
+    if url in SHED_SHORT_NAMES:
+        url = SHED_SHORT_NAMES[url]
+    return url
+
+
+def _tar_excludes(path):
+    name = os.path.basename(path)
+    if name.startswith(".git"):
+        return True
+    elif name in PLANEMO_FILES:
+        return True
+    return False