Fix/update tutorials asset and unitary_event_analysis to use nixio 1.…

…5.0 (#441)

* updated UE tutorial and requirements to use nixio 1.5.0 (#86)

* updated links for datasets used in tutorials asset and UE

* use 'read only' to assure backwards compatibility

* reset outputs of notebook

* remove permalinks from tutorials asset and UE

* hotfix fixed jinja2 version to 3.0.3

* changed URLs to elephant-data master

doc/tutorials/unitary_event_analysis.ipynb

@@ -73,8 +73,8 @@
    },
    "outputs": [],
    "source": [
-    "# Download data\n",
-    "!curl https://web.gin.g-node.org/INM-6/elephant-data/raw/master/dataset-1/dataset-1.h5 --output dataset-1.h5 --location"
+    "# Download trial data\n",
+    "!curl https://gin.g-node.org/INM-6/elephant-data/raw/master/tutorials/tutorial_unitary_event_analysis/data/dataset-1.nix --output dataset-1.nix --location"
    ]
   },
   {
@@ -464,10 +464,13 @@
    },
    "outputs": [],
    "source": [
-    "block = neo.io.NeoHdf5IO(\"./dataset-1.h5\")\n",
-    "sts1 = block.read_block().segments[0].spiketrains\n",
-    "sts2 = block.read_block().segments[1].spiketrains\n",
-    "spiketrains = np.vstack((sts1,sts2)).T"
+    "io = neo.io.NixIO(\"./dataset-1.nix\",'ro')\n",
+    "block = io.read_block()\n",
+    "\n",
+    "spiketrains = []\n",
+    "# each segment contains a single trial\n",
+    "for ind in range(len(block.segments)):\n",
+    "    spiketrains.append (block.segments[ind].spiketrains)"
    ]
   },
   {
@@ -498,9 +501,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "elephant_nixio",
    "language": "python",
-   "name": "python3"
+   "name": "elephant_nixio"
   },
   "language_info": {
    "codemirror_mode": {
@@ -512,7 +515,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.9.7"
   },
   "latex_envs": {
    "LaTeX_envs_menu_present": true,
@@ -574,5 +577,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

requirements/environment-docs.yml

@@ -13,7 +13,7 @@ dependencies:
   - pandas
   - scikit-learn
   - statsmodels
-  - jinja2
+  - jinja2==3.0.3 # prevent bug happening in 3.1.0 for docs
   - pip:
     - neo>=0.10.0
     - viziphant

requirements/requirements-tutorials.txt

@@ -1,4 +1,4 @@
 # Packages required to execute jupyter notebook tutorials
 matplotlib>=3.3.2
 h5py>=3.1.0
-nixio==1.5.0b3
+nixio>=1.5.0