Merge branch 'master' of https://github.com/LorenFrankLab/spyglass in…

…to dev

.github/workflows/test-package-build.yml

@@ -80,15 +80,19 @@ jobs:
       # - name: Run tests
       #   run: pytest --doctest-modules -v --pyargs spyglass
   publish:
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
     needs: [test-package]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spyglass-neuro
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: dist
           path: dist/
-      - uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.vscode/settings.json

@@ -4,11 +4,18 @@
     "files.trimFinalNewlines": true,
     "editor.multiCursorModifier": "ctrlCmd",
     "autoDocstring.docstringFormat": "numpy",
-    "python.formatting.provider": "none",
     "remote.SSH.remoteServerListenOnSocket": true,
     "git.confirmSync": false,
     "python.analysis.typeCheckingMode": "off",
     "[python]": {
-        "editor.defaultFormatter": "ms-python.black-formatter"
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": true
+        },
     },
+    "isort.args": [
+        "--profile",
+        "black"
+    ],
 }

CHANGELOG.md

@@ -4,7 +4,8 @@
 
 - Migrate `config` helper scripts to Spyglass codebase. #662
 - Revise contribution guidelines. #655
-- Minor bug fixes. #656, #657, #659, #651
+- Minor bug fixes. #656, #657, #659, #651, #671
+- Add setup instruction specificity.
 
 ## [0.4.2] (October 10, 2023)
 

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 before importing Spyglass.\n",
+    "\n",
+    "```python\n",
+    "import datajoint as dj\n",
+    "dj.load('/path/to/config')\n",
+    "import spyglass\n",
+    "```"
    ]
   },
   {

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 before importing Spyglass.
+#
+# ```python
+# import datajoint as dj
+# dj.load('/path/to/config')
+# import spyglass
+# ```
 
 # ### Running your own database
 #