Startup quickfixes

CHANGELOG.md

@@ -29,6 +29,7 @@ import all foreign key references.
 ### Infrastructure
 
 - Auto-load within-Spyglass tables for graph operations #1368
+- Add explicit `kachery-cloud` dependency #1430
 
 ### Pipelines
 
@@ -37,6 +38,7 @@ import all foreign key references.
 - Common
     - Add tables for storing optogenetic experiment information #1312
     - Remove wildcard matching in `Nwbfile().get_abs_path` #1382
+    - Ensure `AnalysisNwbfile.get_abs_path` always returns same type #1429
 - Decoding
     - Ensure results directory is created if it doesn't exist #1362
 - Position

environment.yml

@@ -39,4 +39,5 @@ dependencies:
   - pip:
       - ghostipy # for common_filter
       - mountainsort4
+      - kachery-cloud
       - .

environment_dlc.yml

@@ -39,4 +39,5 @@ dependencies:
   - pip:
       - ghostipy # for common_filter
       - mountainsort4
+      - kachery-cloud
       - .[dlc]

environment_moseq_cpu.yml

@@ -39,4 +39,5 @@ dependencies:
   - pip:
       - ghostipy # for common_filter
       - mountainsort4
+      - kachery-cloud
       - .[moseq-cpu]

environment_moseq_gpu.yml

@@ -39,4 +39,5 @@ dependencies:
   - pip:
       - ghostipy # for common_filter
       - mountainsort4
+      - kachery-cloud
       - .[moseq-gpu]

notebooks/00_Setup.ipynb

@@ -502,30 +502,48 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import datajoint as dj\n",
     "from spyglass.settings import SpyglassConfig\n",
     "\n",
-    "# change to the root directory of the project\n",
-    "if os.path.basename(os.getcwd()) == \"notebooks\":\n",
-    "    os.chdir(\"..\")\n",
+    "username = \"your username\"  # replace with username made for you in the spyglass database\n",
+    "initial_password = (\n",
+    "    \"your initial password\"  # replace with the initial password given to you\n",
+    ")\n",
+    "new_password = (\n",
+    "    \"your new password\"  # replace with the new password you want to set\n",
+    ")\n",
+    "spyglass_base_dir = \"/path/like/stelmo/nwb/\"  # replace with a path on your system where spyglass can store NWB files\n",
+    "database_host = \"address like: 'localhost' or 'lmf-db.cin.ucsf.edu'\"\n",
     "\n",
-    "# connect to the database\n",
-    "dj.conn()\n",
     "\n",
-    "# change your password\n",
-    "dj.admin.set_password()\n",
+    "dj.config.update(\n",
+    "    {\n",
+    "        \"database.host\": \"lmf-db.cin.ucsf.edu\",\n",
+    "        \"database.user\": username,\n",
+    "        \"database.password\": initial_password,\n",
+    "        \"database.port\": 3306,\n",
+    "    }\n",
+    ")\n",
+    "\n",
+    "dj.conn()  # connect to the database\n",
+    "\n",
+    "# change your password from the initial password\n",
+    "dj.admin.set_password(new_password, update_config=True)\n",
     "\n",
     "# save the configuration\n",
     "SpyglassConfig().save_dj_config(\n",
-    "    save_method=\"local\",  # global or local\n",
-    "    base_dir=\"/path/like/stelmo/nwb/\",\n",
-    "    database_user=\"your username\",\n",
-    "    database_password=\"your password\",  # remove this line for shared machines\n",
-    "    database_host=\"localhost or lmf-db.cin.ucsf.edu\",  # only list one\n",
+    "    save_method=\"global\",  # global or local\n",
+    "    base_dir=spyglass_base_dir,\n",
+    "    database_user=username,\n",
+    "    database_password=new_password,\n",
+    "    database_host=database_host,  # only list one\n",
     "    database_port=3306,\n",
     "    set_password=False,\n",
-    ")"
+    ")\n",
+    "\n",
+    "# ensure the configuration is saved for future use\n",
+    "dj.config.save_global()\n",
+    "dj.config.save_local()"
    ]
   },
   {

notebooks/py_scripts/00_Setup.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.0
+#       jupytext_version: 1.17.2
 #   kernelspec:
 #     display_name: spyglass
 #     language: python
@@ -426,30 +426,48 @@
 #
 
 # +
-import os
 import datajoint as dj
 from spyglass.settings import SpyglassConfig
 
-# change to the root directory of the project
-if os.path.basename(os.getcwd()) == "notebooks":
-    os.chdir("..")
+username = "your username"  # replace with username made for you in the spyglass database
+initial_password = (
+    "your initial password"  # replace with the initial password given to you
+)
+new_password = (
+    "your new password"  # replace with the new password you want to set
+)
+spyglass_base_dir = "/path/like/stelmo/nwb/"  # replace with a path on your system where spyglass can store NWB files
+database_host = "address like: 'localhost' or 'lmf-db.cin.ucsf.edu'"
+
 
-# connect to the database
-dj.conn()
+dj.config.update(
+    {
+        "database.host": "lmf-db.cin.ucsf.edu",
+        "database.user": username,
+        "database.password": initial_password,
+        "database.port": 3306,
+    }
+)
+
+dj.conn()  # connect to the database
 
-# change your password
-dj.admin.set_password()
+# change your password from the initial password
+dj.admin.set_password(new_password, update_config=True)
 
 # save the configuration
 SpyglassConfig().save_dj_config(
-    save_method="local",  # global or local
-    base_dir="/path/like/stelmo/nwb/",
-    database_user="your username",
-    database_password="your password",  # remove this line for shared machines
-    database_host="localhost or lmf-db.cin.ucsf.edu",  # only list one
+    save_method="global",  # global or local
+    base_dir=spyglass_base_dir,
+    database_user=username,
+    database_password=new_password,
+    database_host=database_host,  # only list one
     database_port=3306,
     set_password=False,
 )
+
+# ensure the configuration is saved for future use
+dj.config.save_global()
+dj.config.save_local()
 # -
 
 # <details><summary>Legacy config</summary>

pyproject.toml

@@ -44,6 +44,7 @@ dependencies = [
     # "ghostipy", # removed from list bc M1 users need to install pyfftw first
     "hdmf>=3.4.6",
     "ipympl",
+    "kachery-cloud",
     "matplotlib",
     "ndx_franklab_novela>=0.1.0",
     "ndx-pose",

src/spyglass/common/common_nwbfile.py

@@ -393,7 +393,7 @@ def get_abs_path(
                 & f"filepath LIKE '%{analysis_nwb_file_name}'"
             )
             if len(query) == 1:  # Else try the standard way
-                return Path(analysis_dir) / query.fetch1("filepath")
+                return str(Path(analysis_dir) / query.fetch1("filepath"))
             logger.warning(
                 f"Found {len(query)} files for: {analysis_nwb_file_name}"
             )