Minor fixes for ipynb notebook tests (#159)

BlueBrain · Jun 24, 2022 · 1d05e4e · 1d05e4e
1 parent 134e6ad
commit 1d05e4e
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Showing 7 changed files with 56 additions and 55 deletions.
diff --git a/bluepysnap/_plotting.py b/bluepysnap/_plotting.py
@@ -369,8 +369,8 @@ def frame_trace(filtered_report, plot_type="mean", ax=None):  # pragma: no cover
         slicer = []
         # create a slicer that will slice only on the last level of the columns
         # that is, node_id for the soma report, element_id for the compartment report
-        for i, _ in enumerate(levels):
-            max_ = levels[i][:max_per_pop][-1]
+        for i, level in enumerate(levels):
+            max_ = level[:max_per_pop][-1]
             slicer.append(slice(None) if i != len(levels) - 1 else slice(None, max_))
         data = filtered_report.report.loc[:, tuple(slicer)].T
         # create [[(pop1, id1), (pop1, id2),...], [(pop2, id1), (pop2, id2),...]]

diff --git a/bluepysnap/edges.py b/bluepysnap/edges.py
@@ -607,7 +607,7 @@ def ids(self, group=None, limit=None, sample=None, raise_missing_property=True):
                     result = [cid.id for cid in result if cid.population == self.name]
                 except AttributeError as e:
                     raise BluepySnapError(
-                        "All values from a list must be of type int or " "CircuitEdgeId."
+                        "All values from a list must be of type int or CircuitEdgeId."
                     ) from e
         if sample is not None:
             if len(result) > 0:

diff --git a/bluepysnap/nodes.py b/bluepysnap/nodes.py
@@ -530,7 +530,7 @@ def ids(self, group=None, limit=None, sample=None, raise_missing_property=True):
                     result = [cid.id for cid in result if cid.population == self.name]
                 except AttributeError as e:
                     raise BluepySnapError(
-                        "All values from a list must be of type int or " "CircuitNodeId."
+                        "All values from a list must be of type int or CircuitNodeId."
                     ) from e
             self._check_ids(result)
             preserve_order = isinstance(group, Sequence)

diff --git a/doc/source/notebooks/01_circuits.ipynb b/doc/source/notebooks/01_circuits.ipynb
@@ -20,21 +20,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "# This step might take some minutes (large file size)\n",
     "\n",
     "from urllib.request import urlretrieve\n",
+    "from pathlib import Path\n",
     "from zipfile import ZipFile\n",
     "\n",
     "url = \"https://zenodo.org/record/6259750/files/thalamus_microcircuit.zip?download=1\"\n",
     "extract_dir=\".\"\n",
     "\n",
-    "zip_path, _ = urlretrieve(url)\n",
-    "with ZipFile(zip_path, \"r\") as f:\n",
-    "    f.extractall(extract_dir)"
+    "circuit_path = Path('./sonata')\n",
+    "if not circuit_path.exists():\n",
+    "    zip_path, _ = urlretrieve(url)\n",
+    "    with ZipFile(zip_path, \"r\") as f:\n",
+    "        f.extractall(extract_dir)"
    ]
   },
   {
@@ -46,7 +49,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -63,7 +66,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -85,34 +88,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
        "{'version': 2,\n",
-       " 'node_sets_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/nodes/node_sets.json',\n",
-       " 'networks': {'nodes': [{'nodes_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/nodes/thalamus_neurons/nodes.h5',\n",
+       " 'node_sets_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/node_sets.json',\n",
+       " 'networks': {'nodes': [{'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/thalamus_neurons/nodes.h5',\n",
        "    'populations': {'thalamus_neurons': {'type': 'biophysical',\n",
        "      'biophysical_neuron_models_dir': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/modelmanagement/20191105/memodels/hoc',\n",
        "      'alternate_morphologies': {'neurolucida-asc': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/ascii',\n",
        "       'h5v1': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/h5'}}}},\n",
-       "   {'nodes_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/nodes/CorticoThalamic_projections/nodes.h5',\n",
+       "   {'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/CorticoThalamic_projections/nodes.h5',\n",
        "    'populations': {'CorticoThalamic_projections': {'type': 'virtual'}}},\n",
-       "   {'nodes_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/nodes/MedialLemniscus_projections/nodes.h5',\n",
+       "   {'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/MedialLemniscus_projections/nodes.h5',\n",
        "    'populations': {'MedialLemniscus_projections': {'type': 'virtual'}}}],\n",
-       "  'edges': [{'edges_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__chemical/edges.h5',\n",
+       "  'edges': [{'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__chemical/edges.h5',\n",
        "    'populations': {'thalamus_neurons__thalamus_neurons__chemical': {'type': 'chemical'}}},\n",
-       "   {'edges_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5',\n",
+       "   {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5',\n",
        "    'populations': {'thalamus_neurons__thalamus_neurons__electrical_synapse': {'type': 'electrical'}}},\n",
-       "   {'edges_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/edges/MedialLemniscus_projections__thalamus_neurons__chemical/edges.h5',\n",
+       "   {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/MedialLemniscus_projections__thalamus_neurons__chemical/edges.h5',\n",
        "    'populations': {'MedialLemniscus_projections__thalamus_neurons__chemical': {'type': 'chemical'}}},\n",
-       "   {'edges_file': '/home/elisabetta/BBP/snap/doc/source/notebooks/sonata/networks/edges/CorticoThalamic_projections__thalamus_neurons__chemical/edges.h5',\n",
+       "   {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/CorticoThalamic_projections__thalamus_neurons__chemical/edges.h5',\n",
        "    'populations': {'CorticoThalamic_projections__thalamus_neurons__chemical': {'type': 'chemical'}}}]}}"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -123,16 +126,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.nodes.Nodes at 0x7f0f10385280>"
+       "<bluepysnap.nodes.Nodes at 0x2aaae172acd0>"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -143,16 +146,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.edges.Edges at 0x7f0f10385250>"
+       "<bluepysnap.edges.Edges at 0x2aaae172a510>"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -163,16 +166,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.node_sets.NodeSets at 0x7f0eddce1070>"
+       "<bluepysnap.node_sets.NodeSets at 0x2aaae1737250>"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -207,9 +210,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/doc/source/notebooks/03_node_properties.ipynb b/doc/source/notebooks/03_node_properties.ipynb
@@ -345,7 +345,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -384,16 +384,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.node_sets.NodeSets at 0x7f7b89144c40>"
+       "<bluepysnap.node_sets.NodeSets at 0x2aaab7ab3df0>"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -411,7 +411,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -459,7 +459,7 @@
        " 'CT_afferents': {'population': 'CorticoThalamic_projections'}}"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -477,7 +477,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -494,10 +494,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {
-    "scrolled": false
-   },
+   "execution_count": 10,
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -545,7 +543,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -582,7 +580,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -591,7 +589,7 @@
        "{'Rt_RC', 'VPL_IN', 'VPL_TC'}"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -609,7 +607,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -622,7 +620,7 @@
        "       ['VPL_IN', 'bAC_IN']], dtype=object)"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -641,7 +639,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -726,7 +724,7 @@
        "28607  mc2;Rt           INH  173.007538  552.684753  837.944153"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }

diff --git a/doc/source/notebooks/04_edge_properties.ipynb b/doc/source/notebooks/04_edge_properties.ipynb
@@ -92,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 3,
    "metadata": {
     "scrolled": true
    },
@@ -140,7 +140,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -172,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,13 +15,13 @@ known_local_folder  =  [
 
 [tool.pylint.messages_control]
 disable = [
-    'bad-continuation',
     'fixme',
     'invalid-name',
     'len-as-condition',
     'no-else-return',
     'import-outside-toplevel',
     'bad-mcs-classmethod-argument',
+    'unnecessary-lambda-assignment',
 ]
 
 [tool.pylint.format]
@@ -43,7 +43,7 @@ max-locals = 15
 max-returns = 6
 
 # Maximum number of branch for function / method body
-max-branchs = 12
+max-branches = 12
 
 # Maximum number of statements in function / method body
 max-statements = 50