Changelog + notebook note on logger

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Refactor restriction use in `delete_downstream_merge` #703
 - Add `cautious_delete` to Mixin class, initial implementation. #711
 - Add `deprecation_factory` to facilitate table migration. #717
+- Add Spyglass logger. #730
 
 ### Pipelines
 

notebooks/00_Setup.ipynb

@@ -41,7 +41,7 @@
     "1. [Python 3.9](https://wiki.python.org/moin/BeginnersGuide/Download).\n",
     "2. [mamba](https://mamba.readthedocs.io/en/latest/installation.html) as a\n",
     "   replacement for conda. Spyglass installation is significantly faster with\n",
-    "   mamba. \n",
+    "   mamba.\n",
     "   ```bash\n",
     "   wget \"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh\"\n",
     "   bash Miniforge3-$(uname)-$(uname -m).sh\n",
@@ -133,7 +133,7 @@
     "```\n",
     "\n",
     "Members of the lab can run the `dj_config.py` helper script to generate a config\n",
-    "like the one below. \n",
+    "like the one below.\n",
     "\n",
     "```bash\n",
     "cd spyglass\n",
@@ -148,17 +148,16 @@
     "[docs](https://lorenfranklab.github.io/spyglass/0.4/installation/) for more\n",
     "information on subdirectories.\n",
     "\n",
-    "A different `output_filename` will save different files: \n",
+    "A different `output_filename` will save different files:\n",
     "\n",
     "- `dj_local_conf.json`: Recommended. Used for tutorials. A file in the current\n",
     "  directory DataJoint will automatically recognize when a Python session is\n",
     "  launched from this directory.\n",
-    "- `.datajoint_config.json` or no input: A file in the user's home directory \n",
+    "- `.datajoint_config.json` or no input: A file in the user's home directory\n",
     "  that will be referenced whenever no local version (see above) is present.\n",
     "- Anything else: A custom name that will need to be loaded (e.g.,\n",
     "  `dj.load('x')`) for each python session.\n",
     "\n",
-    "\n",
     "The config will be a `json` file like the following.\n",
     "\n",
     "```json\n",
@@ -170,6 +169,7 @@
     "    \"database.use_tls\": true,\n",
     "    \"enable_python_native_blobs\": true,\n",
     "    \"filepath_checksum_size_limit\": 1 * 1024**3,\n",
+    "    \"loglevel\": \"INFO\",\n",
     "    \"stores\": {\n",
     "        \"raw\": {\n",
     "            \"protocol\": \"file\",\n",
@@ -190,14 +190,18 @@
     "}\n",
     "```\n",
     "\n",
+    "Spyglass will use the log level present in your DataJoint config to decide the\n",
+    "appropriate logging level for this session. To change the messages you see,\n",
+    "select from one of [these options](https://docs.python.org/3/library/logging.html#levels).\n",
+    "\n",
     "If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your\n",
     "config before importing Spyglass.\n",
     "\n",
     "```python\n",
     "import datajoint as dj\n",
     "dj.load('/path/to/config')\n",
     "import spyglass\n",
-    "```"
+    "```\n"
    ]
   },
   {
@@ -226,8 +230,8 @@
     "  ```\n",
     "\n",
     "_Note_: For this demo, MySQL version won't matter. Some\n",
-    "  [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)\n",
-    "  features of Spyglass, however, expect MySQL >= 8.\n",
+    "[database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)\n",
+    "features of Spyglass, however, expect MySQL >= 8.\n",
     "\n",
     "- When run, this is referred to as a 'Docker container'\n",
     "- Next start the container with a couple additional pieces of info...\n",
@@ -277,7 +281,7 @@
    "source": [
     "### Loading the config\n",
     "\n",
-    "We can check that the paths are correctly set up by loading the config from \n",
+    "We can check that the paths are correctly set up by loading the config from\n",
     "the main Spyglass directory.\n"
    ]
   },
@@ -471,7 +475,7 @@
    "id": "13fd64af",
    "metadata": {},
    "source": [
-    "# Up Next"
+    "# Up Next\n"
    ]
   },
   {

notebooks/py_scripts/00_Setup.py

@@ -135,7 +135,6 @@
 # - Anything else: A custom name that will need to be loaded (e.g.,
 #   `dj.load('x')`) for each python session.
 #
-#
 # The config will be a `json` file like the following.
 #
 # ```json
@@ -147,6 +146,7 @@
 #     "database.use_tls": true,
 #     "enable_python_native_blobs": true,
 #     "filepath_checksum_size_limit": 1 * 1024**3,
+#     "loglevel": "INFO",
 #     "stores": {
 #         "raw": {
 #             "protocol": "file",
@@ -167,6 +167,10 @@
 # }
 # ```
 #
+# Spyglass will use the log level present in your DataJoint config to decide the
+# appropriate logging level for this session. To change the messages you see,
+# select from one of [these options](https://docs.python.org/3/library/logging.html#levels).
+#
 # If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your
 # config before importing Spyglass.
 #
@@ -175,6 +179,7 @@
 # dj.load('/path/to/config')
 # import spyglass
 # ```
+#
 
 # ### Running your own database
 #
@@ -192,8 +197,8 @@
 #   ```
 #
 # _Note_: For this demo, MySQL version won't matter. Some
-#   [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)
-#   features of Spyglass, however, expect MySQL >= 8.
+# [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)
+# features of Spyglass, however, expect MySQL >= 8.
 #
 # - When run, this is referred to as a 'Docker container'
 # - Next start the container with a couple additional pieces of info...
@@ -244,7 +249,6 @@
 
 # +
 import os
-
 import datajoint as dj
 
 if os.path.basename(os.getcwd()) == "notebooks":
@@ -270,6 +274,7 @@
 # -
 
 # # Up Next
+#
 
 # Next, we'll try [inserting data](./01_Insert_Data.ipynb)
 #

src/spyglass/utils/logging.py

@@ -1,11 +1,12 @@
 """Logging configuration based on datajoint/logging.py"""
 import logging
-import os
 import sys
 
+import datajoint as dj
+
 logger = logging.getLogger(__name__.split(".")[0])
 
-log_level = os.getenv("DJ_LOG_LEVEL", "info").upper()
+log_level = dj.config.get("loglevel", "INFO").upper()
 
 log_format = logging.Formatter(
     "[%(asctime)s][%(levelname)s] Spyglass: %(message)s", datefmt="%H:%M:%S"