Merge branch 'main' of github.com:SpikeInterface/MEArec

Author: alejoe91

.github/workflows/python-package.yml

@@ -13,19 +13,20 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.12"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Which conda/python
+      - name: Which python
         run: |
-          conda --version
           python --version
       - name: Install dependencies
         run: |
           pip install .[templates,test]
+          pip install "zarr<3.0.0"
       - name: pip list
         run: |
           pip list

.github/workflows/python-publish.yml

@@ -14,13 +14,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Which python
         run: |
-          conda --version
+          python --version
       - name: Install dependencies
         run: |
           pip install .[templates,test]

notebooks/generate_recordings_with_allen_models.ipynb

@@ -38,7 +38,8 @@
     "import json\n",
     "import matplotlib.pylab as plt\n",
     "from pprint import pprint\n",
-    "%matplotlib notebook"
+    "\n",
+    "%matplotlib inline"
    ]
   },
   {
@@ -141,7 +142,11 @@
     "    ax_xz = fig.add_subplot(2,2,2)    \n",
     "    ax_yz = fig.add_subplot(2,2,3)    \n",
     "    \n",
-    "    for i, (xs, xe, ys, ye, zs, ze) in enumerate(zip(cell.xstart, cell.xend, cell.ystart, cell.yend, cell.zstart, cell.zend)):\n",
+    "    for i in range(len(cell.x)):\n",
+    "        xs, xe = cell.x[i][0], cell.x[i][-1]\n",
+    "        ys, ye = cell.y[i][0], cell.y[i][-1]\n",
+    "        zs, ze = cell.z[i][0], cell.z[i][-1]\n",
+    "        \n",
     "        if i in cell.get_idx('soma'):\n",
     "            ax_xy.plot([xs, xe], [ys, ye], color='k', lw=5)\n",
     "            ax_xz.plot([xs, xe], [zs, ze], color='k', lw=5)\n",
@@ -585,9 +590,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "ax_st = mr.plot_rasters(recgen.spiketrains)\n",
@@ -628,9 +631,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "MEArec"
-version = "1.9.1"
+version = "1.9.2"
 authors = [
   { name="Alessio Buccino", email="[email protected]" },
 ]

readthedocs.yml

@@ -1,5 +1,9 @@
 version: 2
 
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/conf.py
+
 build:
   os: ubuntu-22.04
   tools:

src/MEArec/generators/spiketraingenerator.py

@@ -1,7 +1,5 @@
 from copy import deepcopy
 
-import elephant.spike_train_generation as stg
-import elephant.statistics as stat
 import neo
 import numpy as np
 import quantities as pq
@@ -129,6 +127,9 @@ def generate_spikes(self):
         Generate spike trains based on default_params of the SpikeTrainGenerator class.
         self.spiketrains contains the newly generated spike trains
         """
+        import elephant.spike_train_generation as stg
+        import elephant.statistics as stat
+        
         if not self._has_spiketrains:
             self.spiketrains = []
             idx = 0

src/MEArec/tests/test_generators.py

@@ -4,7 +4,6 @@
 from copy import deepcopy
 from pathlib import Path
 
-import elephant.statistics as stat
 import numpy as np
 import yaml
 from click.testing import CliRunner
@@ -198,6 +197,8 @@ def test_gen_templates_beta_distr(self):
         assert tempgen_drift_beta.templates.shape[0] == self.tempgen_drift.templates.shape[0]
 
     def test_gen_spiketrains(self):
+        import elephant.statistics as stat
+        
         print("Test spike train generation")
         rec_params = mr.get_default_recordings_params()
         sp_params = rec_params["spiketrains"]

src/MEArec/tools.py

@@ -777,7 +777,7 @@ def clean_dict(d):
 def _clean_numpy_scalar(v):
     if isinstance(v, np.bool_):
         v = bool(v)
-    if isinstance(v, np.float_):
+    if isinstance(v, np.float64):
         v = float(v)
     if isinstance(v, np.int_):
         v = int(v)
@@ -3098,7 +3098,7 @@ def plot_templates(
         else:
             colors = plt.rcParams["axes.prop_cycle"].by_key()["color"]
 
-        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax)
+        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax.get_subplotspec())
 
         for i_n, n in enumerate(template_ids):
             r = i_n // ncols
@@ -3318,7 +3318,7 @@ def plot_waveforms(
             nrows = 1
             ncols = n_units
 
-        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax)
+        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax.get_subplotspec())
 
         for i, wf in enumerate(waveforms):
             r = i // ncols
@@ -3336,7 +3336,7 @@ def plot_waveforms(
             nrows = 1
             ncols = len(spiketrain_id)
 
-        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax)
+        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax.get_subplotspec())
 
         # find ylim
         min_wf = 0
@@ -3488,7 +3488,7 @@ def plot_amplitudes(
             nrows = 1
             ncols = n_units
 
-        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax)
+        gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax.get_subplotspec())
 
         for i_n, n in enumerate(spiketrain_id):
             r = i_n // ncols
@@ -3626,7 +3626,7 @@ def plot_pca_map(
 
     nrows = len(pc_dims) * len(elec_dims)
     ncols = nrows
-    gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax)
+    gs = gridspec.GridSpecFromSubplotSpec(nrows, ncols, subplot_spec=ax.get_subplotspec())
 
     for p1 in pc_dims:
         for i1, ch1 in enumerate(elec_dims):