Add a command line flag for controlling systemd user mode

.github/workflows/lint.yaml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.10']
+        python-version: ['3.9', '3.13']
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox

.github/workflows/package.yaml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.10']
+        python-version: ['3.9', '3.13']
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/publish.yaml

@@ -10,9 +10,9 @@ jobs:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Install dependencies

.github/workflows/test.yaml

@@ -10,15 +10,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.9', '3.13']
         galaxy-branch: ['release_23.0', 'dev']
         exclude:
-          # this results in lengthy and expensive numpy wheel builds
-          - python-version: '3.10'
-            galaxy-branch: 'release_22.01'
+          # either the release existed before the python release or some expensive-to-build wheels (e.g. numpy) don't
+          # exist for the pinned package version / python version combo
+          - python-version: '3.13'
+            galaxy-branch: 'release_23.0'
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Precreate virtualenv

gravity/cli.py

@@ -83,11 +83,13 @@ def galaxy(ctx, debug, config_file, state_dir, quiet):
 @options.debug_option()
 @options.config_file_option()
 @options.state_dir_option()
+@options.user_mode_option()
 @click.pass_context
-def galaxyctl(ctx, debug, config_file, state_dir):
+def galaxyctl(ctx, debug, config_file, state_dir, user):
     """Manage Galaxy server configurations and processes."""
     set_debug(debug)
     ctx.cm_kwargs = {
         "config_file": config_file,
         "state_dir": state_dir,
+        "user_mode": user,
     }

gravity/config_manager.py

@@ -35,21 +35,22 @@
 
 
 @contextlib.contextmanager
-def config_manager(config_file=None, state_dir=None):
-    yield ConfigManager(config_file=config_file, state_dir=state_dir)
+def config_manager(config_file=None, state_dir=None, user_mode=None):
+    yield ConfigManager(config_file=config_file, state_dir=state_dir, user_mode=user_mode)
 
 
 class ConfigManager(object):
     galaxy_server_config_section = "galaxy"
     gravity_config_section = "gravity"
     app_config_file_option = "galaxy_config_file"
 
-    def __init__(self, config_file=None, state_dir=None):
+    def __init__(self, config_file=None, state_dir=None, user_mode=None):
         self.__configs = {}
         self.state_dir = None
         if state_dir is not None:
             # convert from pathlib.Path
             self.state_dir = str(state_dir)
+        self.user_mode = user_mode
 
         gravity.io.debug(f"Gravity state dir: {state_dir}")
 

gravity/options.py

@@ -23,6 +23,14 @@ def config_file_option():
     )
 
 
+def user_mode_option():
+    return click.option(
+        "--user/--no-user",
+        default=None,
+        help="Use `systemctl/journalctl --user` (default: automatic depeending on whether run as root)",
+    )
+
+
 def no_log_option():
     return click.option(
         '--quiet', is_flag=True, default=False, help="Only output supervisor logs, do not include process logs"

gravity/process_manager/__init__.py

@@ -65,8 +65,8 @@ def decorator(self, *args, instance_names=None, **kwargs):
 
 
 class BaseProcessExecutionEnvironment(metaclass=ABCMeta):
-    def __init__(self, state_dir=None, config_file=None, config_manager=None, **kwargs):
-        self.config_manager = config_manager or ConfigManager(state_dir=state_dir, config_file=config_file)
+    def __init__(self, state_dir=None, config_file=None, config_manager=None, user_mode=None):
+        self.config_manager = config_manager or ConfigManager(state_dir=state_dir, config_file=config_file, user_mode=user_mode)
         self.tail = which("tail")
 
     @abstractmethod
@@ -291,8 +291,8 @@ def exec(self, config, service, service_instance_number=None, no_exec=False):
 
 
 class ProcessManagerRouter:
-    def __init__(self, state_dir=None, config_file=None, config_manager=None, **kwargs):
-        self.config_manager = config_manager or ConfigManager(state_dir=state_dir, config_file=config_file)
+    def __init__(self, state_dir=None, config_file=None, config_manager=None, user_mode=None, **kwargs):
+        self.config_manager = config_manager or ConfigManager(state_dir=state_dir, config_file=config_file, user_mode=user_mode)
         self._load_pm_modules(**kwargs)
         self._process_executor = ProcessExecutor(config_manager=self.config_manager)
 

gravity/process_manager/systemd.py

@@ -110,7 +110,9 @@ class SystemdProcessManager(BaseProcessManager):
 
     def __init__(self, foreground=False, **kwargs):
         super(SystemdProcessManager, self).__init__(**kwargs)
-        self.user_mode = not self.config_manager.is_root
+        self.user_mode = self.config_manager.user_mode
+        if self.user_mode is None:
+            self.user_mode = not self.config_manager.is_root
 
     @property
     def __systemd_unit_dir(self):