[22.01] Include gravity in sample config

lib/galaxy/config/config_manage.py

@@ -12,6 +12,7 @@
 import requests
 import yaml
 from boltons.iterutils import remap
+from gravity.util import settings_to_sample
 
 try:
     from pykwalify.core import Core
@@ -694,6 +695,8 @@ def _build_sample_yaml(args, app_desc):
         description = description.lstrip()
         as_comment = "\n".join(f"# {line}" for line in description.split("\n")) + "\n"
         f.write(as_comment)
+    if app_desc.app_name == "galaxy":
+        f.write(settings_to_sample())
     _write_sample_section(args, f, 'uwsgi', Schema(UWSGI_OPTIONS), as_comment=False, uwsgi_hack=True)
     _write_sample_section(args, f, app_desc.app_name, schema)
     destination = os.path.join(args.galaxy_root, app_desc.sample_destination)

lib/galaxy/config/sample/galaxy.yml.sample

@@ -16,6 +16,125 @@
 # 
 # Config hackers are encouraged to check there before asking for help.
 # 
+# Configuration for Gravity process manager.
+# ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
+gravity:
+
+  # Specify Galaxy's root directory.
+  # Gravity will attempt to find the root directory, but you can set the directory explicitly with this option.
+  # galaxy_root:
+
+  # Set to a directory that should contain log files for the processes controlled by Gravity.
+  # If not specified defaults to ``<state_dir>/logs``.
+  # log_dir:
+
+  # Set to Galaxy's virtualenv directory.
+  # If not specified, Gravity assumes all processes are on PATH.
+  # virtualenv:
+
+  # Select the application server.
+  # ``gunicorn`` is the default application server.
+  # ``unicornherder`` is a production-oriented manager for (G)unicorn servers that automates zero-downtime Galaxy server restarts,
+  # similar to uWSGI Zerg Mode used in the past.
+  # Valid options are: gunicorn, unicornherder
+  # app_server: gunicorn
+
+  # Override the default instance name.
+  # this is hidden from you when running a single instance.
+  # instance_name: _default_
+
+  # Configuration for Gunicorn.
+  gunicorn:
+
+    # The socket to bind. A string of the form: ``HOST``, ``HOST:PORT``, ``unix:PATH``, ``fd://FD``. An IP is a valid HOST.
+    # bind: localhost:8080
+
+    # Controls the number of Galaxy application processes Gunicorn will spawn.
+    # Increased web performance can be attained by increasing this value.
+    # If Gunicorn is the only application on the server, a good starting value is the number of CPUs * 2 + 1.
+    # 4-12 workers should be able to handle hundreds if not thousands of requests per second.
+    # workers: 1
+
+    # Gunicorn workers silent for more than this many seconds are killed and restarted.
+    # Value is a positive number or 0. Setting it to 0 has the effect of infinite timeouts by disabling timeouts for all workers entirely.
+    # If you disable the ``preload`` option workers need to have finished booting within the timeout.
+    # timeout: 300
+
+    # Extra arguments to pass to Gunicorn command line.
+    # extra_args:
+
+    # Use Gunicorn's --preload option to fork workers after loading the Galaxy Application.
+    # Consumes less memory when multiple processes are configured.
+    # preload: true
+
+  # Configuration for Celery Processes.
+  celery:
+
+    # Number of Celery Workers to start.
+    # concurrency: 2
+
+    # Log Level to use for Celery Worker.
+    # Valid options are: DEBUG, INFO, WARNING, ERROR
+    # loglevel: DEBUG
+
+    # Extra arguments to pass to Celery command line.
+    # extra_args:
+
+  # Configuration for gx-it-proxy.
+  gx_it_proxy:
+
+    # Set to true to start gx-it-proxy
+    # enable: false
+
+    # Public-facing IP of the proxy
+    # ip: localhost
+
+    # Public-facing port of the proxy
+    # port: 4002
+
+    # Routes file to monitor.
+    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section.
+    # sessions: database/interactivetools_map.sqlite
+
+    # Include verbose messages in gx-it-proxy
+    # verbose: true
+
+    # Forward all requests to IP.
+    # This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
+    # forward_ip:
+
+    # Forward all requests to port.
+    # This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
+    # forward_port:
+
+    # Rewrite location blocks with proxy port.
+    # This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
+    # reverse_proxy: false
+
+  # Configuration for tusd server (https://github.com/tus/tusd).
+  # The ``tusd`` binary must be installed manually and made available on PATH (e.g in galaxy's .venv/bin directory).
+  tusd:
+
+    # Enable tusd server.
+    # If enabled, you also need to set up your proxy as outlined in https://docs.galaxyproject.org/en/latest/admin/nginx.html#receiving-files-via-the-tus-protocol.
+    # enable: false
+
+    # Host to bind the tusd server to
+    # host: localhost
+
+    # Port to bind the tusd server to
+    # port: 1080
+
+    # Directory to store uploads in.
+    # Must match ``tus_upload_store`` setting in ``galaxy:`` section.
+    # upload_dir:
+
+    # Extra arguments to pass to tusd command line.
+    # extra_args:
+
+  # Configure dynamic handlers in this section.
+  # See https://docs.galaxyproject.org/en/latest/admin/scaling.html#dynamically-defined-handlers for details.
+  # handlers: {}
 uwsgi:
 
   # The address and port on which to listen.  By default, only listen to

lib/galaxy/dependencies/dev-requirements.txt

@@ -65,7 +65,7 @@ fs==2.4.14
 funcsigs==1.0.2
 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
 galaxy-sequence-utils==1.1.5
-gravity==0.10.0; python_version >= "3.6"
+gravity==0.11.0; python_version >= "3.6"
 greenlet==1.1.2; python_version >= "3" and python_full_version < "3.0.0" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.0") or python_version >= "3" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.0") and python_full_version >= "3.5.0"
 gunicorn==20.1.0; python_version >= "3.5"
 gxformat2==0.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -56,7 +56,7 @@ fs==2.4.14
 funcsigs==1.0.2
 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
 galaxy-sequence-utils==1.1.5
-gravity==0.10.0; python_version >= "3.6"
+gravity==0.11.0; python_version >= "3.6"
 greenlet==1.1.2; python_version >= "3" and python_full_version < "3.0.0" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.0") or python_version >= "3" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.0") and python_full_version >= "3.5.0"
 gunicorn==20.1.0; python_version >= "3.5"
 gxformat2==0.15.0