Merge pull request #264 from Pioreactor/pi-to-pioreactor

change user from pi to pioreactor

CHANGELOG.md

@@ -1,6 +1,11 @@
-### Upcoming
+### 22.4.0
  - store more experiment metadata, like strain and media, in the database.
+ - adding temporary labels of Pioreactors into the database in `pioreactor_unit_labels` table
+ - renaming some tables, `alt_media_fraction` -> `alt_media_fractions`, `ir_led_intensity` -> `ir_led_intensities`
  - pumps now throw a `CalibrationError` exception if their calibration is not defined.
+ - default user is no longer `pi`. It is now `pioreactor`. Any coded paths like `/home/pi/` should be updated to `home/pioreactor/`.
+ - new image metadata file added to `home/pioreactor/.pioreactor/.image_metadata`
+
 
 ### 22.3.0
  - fixed memory leak in MQTT connections

pioreactor/actions/leader/backup_database.py

@@ -1,17 +1,19 @@
 # -*- coding: utf-8 -*-
+from __future__ import annotations
+
 from time import sleep
 
 import click
 
-from pioreactor.config import config, get_active_workers_in_inventory
+from pioreactor.config import config
+from pioreactor.config import get_active_workers_in_inventory
 from pioreactor.logging import create_logger
+from pioreactor.utils import is_pio_job_running
+from pioreactor.utils import local_persistant_storage
+from pioreactor.utils import publish_ready_to_disconnected_state
 from pioreactor.utils.timing import current_utc_time
-from pioreactor.utils import (
-    local_persistant_storage,
-    is_pio_job_running,
-    publish_ready_to_disconnected_state,
-)
-from pioreactor.whoami import get_unit_name, UNIVERSAL_EXPERIMENT
+from pioreactor.whoami import get_unit_name
+from pioreactor.whoami import UNIVERSAL_EXPERIMENT
 
 
 def backup_database(output_file: str) -> None:
@@ -93,7 +95,9 @@ def progress(status: int, remaining: int, total: int) -> None:
 
 
 @click.command(name="backup_database")
-@click.option("--output", default="/home/pi/.pioreactor/storage/pioreactor.sqlite.backup")
+@click.option(
+    "--output", default="/home/pioreactor/.pioreactor/storage/pioreactor.sqlite.backup"
+)
 def click_backup_database(output: str) -> None:
     """
     (leader only) Backup db to workers.

pioreactor/actions/leader/export_experiment_data.py

@@ -100,7 +100,7 @@ def export_experiment_data(experiment: str, output: str, tables: list) -> None:
 
 @click.command(name="export_experiment_data")
 @click.option("--experiment", default=None)
-@click.option("--output", default="/home/pi/exports/export.zip")
+@click.option("--output", default="/home/pioreactor/exports/export.zip")
 @click.option("--tables", multiple=True, default=[])
 def click_export_experiment_data(experiment, output, tables):
     """

pioreactor/background_jobs/base.py

@@ -659,6 +659,8 @@ def lost(self) -> None:
 
     def _cleanup(self):
         # Explicitly cleanup resources...
+        # it's pretty slow to disconnect from MQTT. Takes up to ~1 second. We do it three times here:
+        # logger, sub_client, pub_client.
 
         # clean up logger handlers
         while len(self.logger.handlers) > 0:

pioreactor/cli/pios.py

@@ -50,11 +50,11 @@ def save_config_files_to_db(units: tuple[str, ...], shared: bool, specific: bool
 
     if specific:
         for unit in units:
-            with open(f"/home/pi/.pioreactor/config_{unit}.ini") as f:
+            with open(f"/home/pioreactor/.pioreactor/config_{unit}.ini") as f:
                 cur.execute(sql, (timestamp, f"config_{unit}.ini", f.read()))
 
     if shared:
-        with open("/home/pi/.pioreactor/config.ini") as f:
+        with open("/home/pioreactor/.pioreactor/config.ini") as f:
             cur.execute(sql, (timestamp, "config.ini", f.read()))
 
     conn.commit()
@@ -74,16 +74,16 @@ def sync_config_files(ftp_client, unit: str, shared: bool, specific: bool) -> No
     # there was a bug where if the leader == unit, the config.ini would get wiped
     if (get_leader_hostname() != unit) and shared:
         ftp_client.put(
-            localpath="/home/pi/.pioreactor/config.ini",
-            remotepath="/home/pi/.pioreactor/config.ini",
+            localpath="/home/pioreactor/.pioreactor/config.ini",
+            remotepath="/home/pioreactor/.pioreactor/config.ini",
         )
 
     # move the specific unit config.ini
     if specific:
         try:
             ftp_client.put(
-                localpath=f"/home/pi/.pioreactor/config_{unit}.ini",
-                remotepath="/home/pi/.pioreactor/unit_config.ini",
+                localpath=f"/home/pioreactor/.pioreactor/config_{unit}.ini",
+                remotepath="/home/pioreactor/.pioreactor/unit_config.ini",
             )
         except Exception as e:
             click.echo(

pioreactor/config.py

@@ -105,11 +105,11 @@ def get_config():
         global_config_path = "./config.dev.ini"
         local_config_path = ""
     else:
-        global_config_path = "/home/pi/.pioreactor/config.ini"
-        local_config_path = "/home/pi/.pioreactor/unit_config.ini"
+        global_config_path = "/home/pioreactor/.pioreactor/config.ini"
+        local_config_path = "/home/pioreactor/.pioreactor/unit_config.ini"
         if not os.path.isfile(global_config_path):
             raise FileNotFoundError(
-                "/home/pi/.pioreactor/config.ini is missing from this Pioreactor. Has it completed initializing? Does it need to connect to a leader?"
+                "/home/pioreactor/.pioreactor/config.ini is missing from this Pioreactor. Has it completed initializing? Does it need to connect to a leader?"
             )
 
     config_files = [global_config_path, local_config_path]
@@ -122,7 +122,7 @@ def get_config():
         # pios sync tries to run, it uses a malformed unit_config.ini and hence the leader_config.ini can't be deployed
         # to replace the malformed unit_config.ini.
         print(
-            "Bad config state. Check /home/pi/.pioreactor/unit_config.ini on leader for malformed configuration?"
+            "Bad config state. Check /home/pioreactor/.pioreactor/unit_config.ini on leader for malformed configuration?"
         )
         raise e
     except configparser.DuplicateSectionError as e:

pioreactor/plugin_management/__init__.py

@@ -93,7 +93,7 @@ def get_plugins() -> dict[str, Plugin]:
     if is_testing_env():
         MODULE_DIR = "plugins_dev"
     else:
-        MODULE_DIR = "/home/pi/.pioreactor/plugins"
+        MODULE_DIR = "/home/pioreactor/.pioreactor/plugins"
 
     sys.path.append(MODULE_DIR)
 

pioreactor/utils/__init__.py

@@ -203,7 +203,7 @@ def local_persistant_storage(
         if is_testing_env():
             cache = ndbm.open(f".pioreactor/storage/{cache_name}", "c")
         else:
-            cache = ndbm.open(f"/home/pi/.pioreactor/storage/{cache_name}", "c")
+            cache = ndbm.open(f"/home/pioreactor/.pioreactor/storage/{cache_name}", "c")
         yield cache  # type: ignore
     finally:
         cache.close()

pioreactor/version.py

@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 
-__version__ = "22.3.0"
+__version__ = "22.4.0"
 
 
 def _get_hardware_version() -> tuple[int, int]: