Add setup specificity

CBroz1 · Nov 3, 2023 · 1848da3 · 1848da3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 - Migrate `config` helper scripts to Spyglass codebase. #662
 - Revise contribution guidelines. #655
 - Minor bug fixes. #656, #657, #659, #651, #671
+- Add setup instruction specificity.
 
 ## [0.4.2] (October 10, 2023)
 

diff --git a/notebooks/00_Setup.ipynb b/notebooks/00_Setup.ipynb
@@ -41,7 +41,11 @@
     "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",
+    "   ```\n",
     "3. [VS Code](https://code.visualstudio.com/docs/python/python-tutorial) with\n",
     "   relevant python extensions, including\n",
     "   [Jupyter](https://code.visualstudio.com/docs/datascience/jupyter-notebooks).\n",
@@ -119,14 +123,26 @@
    "id": "580d3feb",
    "metadata": {},
    "source": [
-    "Members of the Frank Lab can run the `dj_config.py` helper script to generate\n",
-    "a config like the one below. Outside users should copy/paste `dj_local_conf_example` and adjust values accordingly.\n",
+    "Members of the Frank Lab will need to use DataJoint 0.14.2 (currently in\n",
+    "pre-release) in order to change their password on the MySQL 8 server. DataJoint\n",
+    "0.14.2\n",
+    "\n",
+    "```bash\n",
+    "git clone https://github.com/datajoint/datajoint-python\n",
+    "pip install ./datajoint-python\n",
+    "```\n",
+    "\n",
+    "Members of the lab can run the `dj_config.py` helper script to generate a config\n",
+    "like the one below. \n",
     "\n",
     "```bash\n",
     "cd spyglass\n",
     "python config/dj_config.py <username> <base_path> <output_filename>\n",
     "```\n",
     "\n",
+    "Outside users should copy/paste `dj_local_conf_example` and adjust values\n",
+    "accordingly.\n",
+    "\n",
     "The base path (formerly `SPYGLASS_BASE_DIR`) is the directory where all data\n",
     "will be saved. See also\n",
     "[docs](https://lorenfranklab.github.io/spyglass/0.4/installation/) for more\n",
@@ -172,7 +188,16 @@
     "        }\n",
     "    }\n",
     "}\n",
-    "```\n"
+    "```\n",
+    "\n",
+    "If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your\n",
+    "config befor importing Spyglass.\n",
+    "\n",
+    "```python\n",
+    "import datajoint as dj\n",
+    "dj.load('/path/to/config')\n",
+    "import spyglass\n",
+    "```"
    ]
   },
   {

diff --git a/notebooks/py_scripts/00_Setup.py b/notebooks/py_scripts/00_Setup.py
@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.15.2
+#       jupytext_version: 1.14.5
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -39,6 +39,10 @@
 # 2. [mamba](https://mamba.readthedocs.io/en/latest/installation.html) as a
 #    replacement for conda. Spyglass installation is significantly faster with
 #    mamba.
+#    ```bash
+#    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+#    bash Miniforge3-$(uname)-$(uname -m).sh
+#    ```
 # 3. [VS Code](https://code.visualstudio.com/docs/python/python-tutorial) with
 #    relevant python extensions, including
 #    [Jupyter](https://code.visualstudio.com/docs/datascience/jupyter-notebooks).
@@ -96,14 +100,26 @@
 # ### Existing Database
 #
 
-# Members of the Frank Lab can run the `dj_config.py` helper script to generate
-# a config like the one below. Outside users should copy/paste `dj_local_conf_example` and adjust values accordingly.
+# Members of the Frank Lab will need to use DataJoint 0.14.2 (currently in
+# pre-release) in order to change their password on the MySQL 8 server. DataJoint
+# 0.14.2
+#
+# ```bash
+# git clone https://github.com/datajoint/datajoint-python
+# pip install ./datajoint-python
+# ```
+#
+# Members of the lab can run the `dj_config.py` helper script to generate a config
+# like the one below.
 #
 # ```bash
 # # cd spyglass
 # python config/dj_config.py <username> <base_path> <output_filename>
 # ```
 #
+# Outside users should copy/paste `dj_local_conf_example` and adjust values
+# accordingly.
+#
 # The base path (formerly `SPYGLASS_BASE_DIR`) is the directory where all data
 # will be saved. See also
 # [docs](https://lorenfranklab.github.io/spyglass/0.4/installation/) for more
@@ -151,6 +167,14 @@
 # }
 # ```
 #
+# If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your
+# config befor importing Spyglass.
+#
+# ```python
+# import datajoint as dj
+# dj.load('/path/to/config')
+# import spyglass
+# ```
 
 # ### Running your own database
 #