From 57f4c75ec5a492d36250f1c4ffe28a2ae2d0d0fe Mon Sep 17 00:00:00 2001
From: 1uc <luc.grosheintz@gmail.com>
Date: Wed, 22 May 2024 07:51:34 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BlueBrai?=
 =?UTF-8?q?n/nmodl@f28a335a798b7b12b9bdc2027be3f37e32f3eb29=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .doctrees/contributing.doctree                | Bin 64130 -> 64130 bytes
 .doctrees/environment.pickle                  | Bin 131572 -> 133088 bytes
 .doctrees/install.doctree                     | Bin 70599 -> 70599 bytes
 .../notebooks/nmodl-kinetic-schemes.ipynb     |  56 +++---
 .../notebooks/nmodl-python-tutorial.ipynb     | 160 +++++++++---------
 .../notebooks/nmodl-sympy-conductance.ipynb   |  72 ++++----
 .../notebooks/nmodl-sympy-solver-cnexp.ipynb  |  81 +++++----
 .../nmodl-sympy-solver-derivimplicit.ipynb    |  32 ++--
 .../notebooks/nmodl-sympy-solver-sparse.ipynb |  32 ++--
 .doctrees/nmodl.doctree                       | Bin 87358 -> 87577 bytes
 .doctrees/readme.doctree                      | Bin 174287 -> 175803 bytes
 _modules/nmodl/ode.html                       |  71 ++++++--
 genindex.html                                 |   4 +-
 modules.html                                  |   4 +-
 nmodl.html                                    |  12 +-
 notebooks/nmodl-kinetic-schemes.ipynb         |  56 +++---
 notebooks/nmodl-python-tutorial.ipynb         | 160 +++++++++---------
 notebooks/nmodl-sympy-conductance.ipynb       |  72 ++++----
 notebooks/nmodl-sympy-solver-cnexp.ipynb      |  81 +++++----
 .../nmodl-sympy-solver-derivimplicit.ipynb    |  32 ++--
 notebooks/nmodl-sympy-solver-sparse.ipynb     |  32 ++--
 objects.inv                                   | Bin 3514 -> 3520 bytes
 searchindex.js                                |   2 +-
 23 files changed, 515 insertions(+), 444 deletions(-)

diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
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diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree
index 6568fd523902ad844c465069c5287875d15e447c..48a8bab1da42e2d2b3666bfc11c198375be8a2e6 100644
GIT binary patch
delta 2587
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diff --git a/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb
index 43c159f56d..810e29d749 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb
@@ -152,10 +152,10 @@
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@@ -169,10 +169,10 @@
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@@ -277,10 +277,10 @@
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@@ -323,10 +323,10 @@
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@@ -367,10 +367,10 @@
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@@ -412,10 +412,10 @@
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@@ -459,10 +459,10 @@
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diff --git a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb
index ceb94c6573..561b865213 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb
@@ -30,10 +30,10 @@
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@@ -63,10 +63,10 @@
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@@ -86,10 +86,10 @@
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@@ -152,10 +152,10 @@
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@@ -183,10 +183,10 @@
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@@ -235,10 +235,10 @@
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@@ -260,10 +260,10 @@
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@@ -297,10 +297,10 @@
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@@ -365,10 +365,10 @@
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@@ -416,10 +416,10 @@
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@@ -441,10 +441,10 @@
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@@ -510,10 +510,10 @@
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@@ -548,10 +548,10 @@
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@@ -584,10 +584,10 @@
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@@ -622,10 +622,10 @@
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@@ -669,10 +669,10 @@
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@@ -733,10 +733,10 @@
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    "metadata": {
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    "outputs": [],
@@ -761,10 +761,10 @@
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    "metadata": {
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@@ -857,10 +857,10 @@
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     }
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    "outputs": [
@@ -897,10 +897,10 @@
    "execution_count": 20,
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     }
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    "outputs": [
diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb
index 63d6968f17..da91eecd2c 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb
@@ -86,10 +86,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
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-     "shell.execute_reply": "2024-05-21T21:13:54.050468Z"
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     }
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    "outputs": [],
@@ -103,10 +103,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.054259Z",
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-     "shell.execute_reply": "2024-05-21T21:13:54.080493Z"
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     }
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@@ -149,10 +149,10 @@
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    "metadata": {
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-     "shell.execute_reply": "2024-05-21T21:13:54.360852Z"
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    "outputs": [
@@ -196,10 +196,10 @@
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     }
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    "outputs": [
@@ -243,10 +243,10 @@
    "execution_count": 5,
    "metadata": {
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-     "shell.execute_reply": "2024-05-21T21:13:54.521906Z"
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@@ -290,10 +290,10 @@
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-     "shell.execute_reply": "2024-05-21T21:13:54.541015Z"
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    "outputs": [
@@ -337,10 +337,10 @@
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    "metadata": {
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@@ -400,10 +400,10 @@
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@@ -456,10 +456,10 @@
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     }
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    "outputs": [
diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb
index 614e432167..424e177840 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb
@@ -62,10 +62,10 @@
    "execution_count": 1,
    "metadata": {
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-     "shell.execute_reply": "2024-05-21T21:13:58.044630Z"
+     "iopub.execute_input": "2024-05-22T07:51:02.331013Z",
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     }
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    "outputs": [],
@@ -79,10 +79,10 @@
    "execution_count": 2,
    "metadata": {
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-     "iopub.execute_input": "2024-05-21T21:13:58.048672Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.048281Z",
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-     "shell.execute_reply": "2024-05-21T21:13:58.075220Z"
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     }
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    "outputs": [],
@@ -123,10 +123,10 @@
    "execution_count": 3,
    "metadata": {
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-     "iopub.execute_input": "2024-05-21T21:13:58.079692Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.079187Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.503645Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.502915Z"
+     "iopub.execute_input": "2024-05-22T07:51:03.678502Z",
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+     "shell.execute_reply": "2024-05-22T07:51:04.101410Z"
     }
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    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
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-     "iopub.execute_input": "2024-05-21T21:13:58.506498Z",
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-     "shell.execute_reply": "2024-05-21T21:13:58.635986Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.104749Z",
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+     "shell.execute_reply": "2024-05-22T07:51:04.233059Z"
     }
    },
    "outputs": [
@@ -207,10 +207,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.639552Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.639091Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.869674Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.868909Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.236684Z",
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     }
    },
    "outputs": [
@@ -218,7 +218,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "exact solution:\t     m = minf-(-m+minf)*exp(-dt/mtau)\n"
+      "exact solution:\t"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "     m = minf-(-m+minf)*exp(-dt/mtau)\n"
      ]
     },
     {
@@ -255,10 +262,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
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+     "iopub.status.busy": "2024-05-22T07:51:04.468973Z",
+     "iopub.status.idle": "2024-05-22T07:51:04.658425Z",
+     "shell.execute_reply": "2024-05-22T07:51:04.657708Z"
     }
    },
    "outputs": [
@@ -266,7 +273,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "exact solution:\t     m = minf+(m-minf)*exp(dt/mtau)\n",
+      "exact solution:\t     m = minf+(m-minf)*exp(dt/mtau)\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "pade approx:\t     m = (-dt*m+2.0*dt*minf-2.0*m*mtau)/(dt-2.0*mtau)\n"
      ]
     }
@@ -297,10 +310,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:59.064836Z",
-     "iopub.status.busy": "2024-05-21T21:13:59.064376Z",
-     "iopub.status.idle": "2024-05-21T21:14:00.452222Z",
-     "shell.execute_reply": "2024-05-21T21:14:00.451520Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.661370Z",
+     "iopub.status.busy": "2024-05-22T07:51:04.660943Z",
+     "iopub.status.idle": "2024-05-22T07:51:06.047306Z",
+     "shell.execute_reply": "2024-05-22T07:51:06.046692Z"
     }
    },
    "outputs": [
@@ -345,10 +358,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:00.454829Z",
-     "iopub.status.busy": "2024-05-21T21:14:00.454433Z",
-     "iopub.status.idle": "2024-05-21T21:14:02.255109Z",
-     "shell.execute_reply": "2024-05-21T21:14:02.254377Z"
+     "iopub.execute_input": "2024-05-22T07:51:06.049973Z",
+     "iopub.status.busy": "2024-05-22T07:51:06.049557Z",
+     "iopub.status.idle": "2024-05-22T07:51:07.832398Z",
+     "shell.execute_reply": "2024-05-22T07:51:07.831659Z"
     }
    },
    "outputs": [
diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
index de660565d2..ceda497eef 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
@@ -39,10 +39,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:03.901559Z",
-     "iopub.status.busy": "2024-05-21T21:14:03.901362Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.216294Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.215535Z"
+     "iopub.execute_input": "2024-05-22T07:51:09.398526Z",
+     "iopub.status.busy": "2024-05-22T07:51:09.398326Z",
+     "iopub.status.idle": "2024-05-22T07:51:10.733117Z",
+     "shell.execute_reply": "2024-05-22T07:51:10.732364Z"
     }
    },
    "outputs": [],
@@ -56,10 +56,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.219326Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.219069Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.246901Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.246266Z"
+     "iopub.execute_input": "2024-05-22T07:51:10.736274Z",
+     "iopub.status.busy": "2024-05-22T07:51:10.735844Z",
+     "iopub.status.idle": "2024-05-22T07:51:10.764120Z",
+     "shell.execute_reply": "2024-05-22T07:51:10.763477Z"
     }
    },
    "outputs": [],
@@ -100,10 +100,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.250032Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.249553Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.712690Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.712004Z"
+     "iopub.execute_input": "2024-05-22T07:51:10.767000Z",
+     "iopub.status.busy": "2024-05-22T07:51:10.766771Z",
+     "iopub.status.idle": "2024-05-22T07:51:11.233306Z",
+     "shell.execute_reply": "2024-05-22T07:51:11.232563Z"
     }
    },
    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.715287Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.715034Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.924246Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.923582Z"
+     "iopub.execute_input": "2024-05-22T07:51:11.235831Z",
+     "iopub.status.busy": "2024-05-22T07:51:11.235569Z",
+     "iopub.status.idle": "2024-05-22T07:51:11.447741Z",
+     "shell.execute_reply": "2024-05-22T07:51:11.447008Z"
     }
    },
    "outputs": [
diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb
index e23506ee2a..3dec84bbbc 100644
--- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb
+++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb
@@ -39,10 +39,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:07.178173Z",
-     "iopub.status.busy": "2024-05-21T21:14:07.177713Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.484640Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.483861Z"
+     "iopub.execute_input": "2024-05-22T07:51:12.891134Z",
+     "iopub.status.busy": "2024-05-22T07:51:12.890591Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.214689Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.213944Z"
     }
    },
    "outputs": [],
@@ -56,10 +56,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.488009Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.487560Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.514113Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.513543Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.217973Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.217528Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.243870Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.243286Z"
     }
    },
    "outputs": [],
@@ -100,10 +100,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.516782Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.516468Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.980321Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.979573Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.246960Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.246408Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.710041Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.709339Z"
     }
    },
    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.983046Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.982759Z",
-     "iopub.status.idle": "2024-05-21T21:14:09.200346Z",
-     "shell.execute_reply": "2024-05-21T21:14:09.199627Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.713086Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.712493Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.923334Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.922620Z"
     }
    },
    "outputs": [
diff --git a/.doctrees/nmodl.doctree b/.doctrees/nmodl.doctree
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diff --git a/.doctrees/readme.doctree b/.doctrees/readme.doctree
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GIT binary patch
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diff --git a/_modules/nmodl/ode.html b/_modules/nmodl/ode.html
index bdf5fc4774..1902bcd2e3 100644
--- a/_modules/nmodl/ode.html
+++ b/_modules/nmodl/ode.html
@@ -136,10 +136,20 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
 <span class="k">if</span> <span class="ow">not</span> <span class="p">((</span><span class="n">major</span> <span class="o">&gt;=</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">minor</span> <span class="o">&gt;=</span> <span class="mi">2</span><span class="p">)):</span>
     <span class="k">raise</span> <span class="ne">ImportError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Requires SympPy version &gt;= 1.2, found </span><span class="si">{</span><span class="n">major</span><span class="si">}</span><span class="s2">.</span><span class="si">{</span><span class="n">minor</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
-<span class="c1"># Some functions are protected inside sympy, if user has declared such a function, it will fail</span>
-<span class="c1"># because sympy will try to use its own internal one.</span>
-<span class="c1"># Rename it before and after to a single name</span>
+<span class="c1"># Some identifiers are protected inside sympy, if user has declared such a function, it will fail</span>
+<span class="c1"># because sympy will try to use its own internal one; or error out for invalid variables.</span>
+<span class="c1"># Rename it before and after to a unique name.</span>
 <span class="n">forbidden_var</span> <span class="o">=</span> <span class="p">[</span>
+    <span class="c1"># Selected Python keywords</span>
+    <span class="s2">&quot;is&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;as&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;count&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;del&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;elif&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;in&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;lambda&quot;</span><span class="p">,</span>
+    <span class="s2">&quot;pass&quot;</span><span class="p">,</span>
+    <span class="c1"># SymPy functions</span>
     <span class="s2">&quot;beta&quot;</span><span class="p">,</span>
     <span class="s2">&quot;gamma&quot;</span><span class="p">,</span>
     <span class="s2">&quot;uppergamma&quot;</span><span class="p">,</span>
@@ -151,21 +161,56 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
 <span class="p">]</span>
 
 
-<div class="viewcode-block" id="search_and_replace_protected_functions_to_sympy"><a class="viewcode-back" href="../../nmodl.html#nmodl.ode.search_and_replace_protected_functions_to_sympy">[docs]</a><span class="k">def</span> <span class="nf">search_and_replace_protected_functions_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
+<div class="viewcode-block" id="search_and_replace_protected_identifiers_to_sympy"><a class="viewcode-back" href="../../nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_to_sympy">[docs]</a><span class="k">def</span> <span class="nf">search_and_replace_protected_identifiers_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
+    <span class="n">eqs</span> <span class="o">=</span> <span class="n">_search_and_replace_protected_functions_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
+    <span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span> <span class="o">=</span> <span class="n">_search_and_replace_protected_variables_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span></div>
+
+
+<div class="viewcode-block" id="search_and_replace_protected_identifiers_from_sympy"><a class="viewcode-back" href="../../nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_from_sympy">[docs]</a><span class="k">def</span> <span class="nf">search_and_replace_protected_identifiers_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
+    <span class="n">eqs</span> <span class="o">=</span> <span class="n">_search_and_replace_protected_functions_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
+    <span class="n">eqs</span> <span class="o">=</span> <span class="n">_search_and_replace_protected_variables_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">eqs</span></div>
+
+
+<span class="k">def</span> <span class="nf">_search_and_replace_protected_variables_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span><span class="p">):</span>
+    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">forbidden_var</span><span class="p">:</span>
+        <span class="n">r</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\b</span><span class="si">{}</span><span class="s2">\b&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">c</span><span class="p">))</span>
+        <span class="n">f</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;_sympy_</span><span class="si">{</span><span class="n">c</span><span class="si">}</span><span class="s2">_var&quot;</span>
+        <span class="n">eqs</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">eqs</span><span class="p">]</span>
+        <span class="nb">vars</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">vars</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">eqs</span><span class="p">,</span> <span class="nb">vars</span>
+
+
+<span class="k">def</span> <span class="nf">_search_and_replace_protected_variables_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">):</span>
+    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">forbidden_var</span><span class="p">:</span>
+        <span class="n">r</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\b_sympy_</span><span class="si">{}</span><span class="s2">_var\b&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">c</span><span class="p">))</span>
+        <span class="n">f</span> <span class="o">=</span> <span class="n">c</span>
+        <span class="n">eqs</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">eqs</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">eqs</span>
+
+
+<span class="k">def</span> <span class="nf">_search_and_replace_protected_functions_to_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
     <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">function_calls</span><span class="p">:</span>
         <span class="k">if</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">forbidden_var</span><span class="p">:</span>
             <span class="n">r</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\b</span><span class="si">{}</span><span class="s2">\b\s*\(&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">c</span><span class="p">))</span>
             <span class="n">f</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;_sympy_</span><span class="si">{</span><span class="n">c</span><span class="si">}</span><span class="s2">_fun(&quot;</span>
             <span class="n">eqs</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">eqs</span><span class="p">]</span>
-    <span class="k">return</span> <span class="n">eqs</span></div>
+
+    <span class="k">return</span> <span class="n">eqs</span>
 
 
-<div class="viewcode-block" id="search_and_replace_protected_functions_from_sympy"><a class="viewcode-back" href="../../nmodl.html#nmodl.ode.search_and_replace_protected_functions_from_sympy">[docs]</a><span class="k">def</span> <span class="nf">search_and_replace_protected_functions_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">_search_and_replace_protected_functions_from_sympy</span><span class="p">(</span><span class="n">eqs</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">):</span>
     <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">function_calls</span><span class="p">:</span>
         <span class="k">if</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">forbidden_var</span><span class="p">:</span>
             <span class="n">r</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;_sympy_</span><span class="si">{</span><span class="n">c</span><span class="si">}</span><span class="s2">_fun&quot;</span>
             <span class="n">eqs</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">c</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">eqs</span><span class="p">]</span>
-    <span class="k">return</span> <span class="n">eqs</span></div>
+
+    <span class="k">return</span> <span class="n">eqs</span>
 
 
 <span class="k">def</span> <span class="nf">_get_custom_functions</span><span class="p">(</span><span class="n">fcts</span><span class="p">):</span>
@@ -367,8 +412,8 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
 <span class="sd">        vars: list of strings containing new local variables</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="n">eq_strings</span> <span class="o">=</span> <span class="n">search_and_replace_protected_functions_to_sympy</span><span class="p">(</span>
-        <span class="n">eq_strings</span><span class="p">,</span> <span class="n">function_calls</span>
+    <span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span> <span class="o">=</span> <span class="n">search_and_replace_protected_identifiers_to_sympy</span><span class="p">(</span>
+        <span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span><span class="p">,</span> <span class="n">function_calls</span>
     <span class="p">)</span>
 
     <span class="n">eqs</span><span class="p">,</span> <span class="n">state_vars</span><span class="p">,</span> <span class="n">sympy_vars</span> <span class="o">=</span> <span class="n">_sympify_eqs</span><span class="p">(</span><span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span><span class="p">,</span> <span class="n">constants</span><span class="p">)</span>
@@ -423,7 +468,7 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
         <span class="c1"># interweave</span>
         <span class="n">code</span> <span class="o">=</span> <span class="n">_interweave_eqs</span><span class="p">(</span><span class="n">vecFcode</span><span class="p">,</span> <span class="n">vecJcode</span><span class="p">)</span>
 
-    <span class="n">code</span> <span class="o">=</span> <span class="n">search_and_replace_protected_functions_from_sympy</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
+    <span class="n">code</span> <span class="o">=</span> <span class="n">search_and_replace_protected_identifiers_from_sympy</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">code</span><span class="p">,</span> <span class="n">new_local_vars</span></div>
 
@@ -445,8 +490,8 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
 <span class="sd">        List of strings containing assignment statements</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="n">eq_strings</span> <span class="o">=</span> <span class="n">search_and_replace_protected_functions_to_sympy</span><span class="p">(</span>
-        <span class="n">eq_strings</span><span class="p">,</span> <span class="n">function_calls</span>
+    <span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span> <span class="o">=</span> <span class="n">search_and_replace_protected_identifiers_to_sympy</span><span class="p">(</span>
+        <span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span><span class="p">,</span> <span class="n">function_calls</span>
     <span class="p">)</span>
 
     <span class="n">eqs</span><span class="p">,</span> <span class="n">state_vars</span><span class="p">,</span> <span class="n">sympy_vars</span> <span class="o">=</span> <span class="n">_sympify_eqs</span><span class="p">(</span><span class="n">eq_strings</span><span class="p">,</span> <span class="nb">vars</span><span class="p">,</span> <span class="n">constants</span><span class="p">)</span>
@@ -475,7 +520,7 @@ <h1>Source code for nmodl.ode</h1><div class="highlight"><pre>
     <span class="c1"># interweave</span>
     <span class="n">code</span> <span class="o">=</span> <span class="n">_interweave_eqs</span><span class="p">(</span><span class="n">vecFcode</span><span class="p">,</span> <span class="n">vecJcode</span><span class="p">)</span>
 
-    <span class="n">code</span> <span class="o">=</span> <span class="n">search_and_replace_protected_functions_from_sympy</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
+    <span class="n">code</span> <span class="o">=</span> <span class="n">search_and_replace_protected_identifiers_from_sympy</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">function_calls</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">code</span></div>
 
diff --git a/genindex.html b/genindex.html
index a441a1ba4c..487b2204aa 100644
--- a/genindex.html
+++ b/genindex.html
@@ -259,9 +259,9 @@ <h2 id="P">P</h2>
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="nmodl.html#nmodl.ode.search_and_replace_protected_functions_from_sympy">search_and_replace_protected_functions_from_sympy() (in module nmodl.ode)</a>
+      <li><a href="nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_from_sympy">search_and_replace_protected_identifiers_from_sympy() (in module nmodl.ode)</a>
 </li>
-      <li><a href="nmodl.html#nmodl.ode.search_and_replace_protected_functions_to_sympy">search_and_replace_protected_functions_to_sympy() (in module nmodl.ode)</a>
+      <li><a href="nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_to_sympy">search_and_replace_protected_identifiers_to_sympy() (in module nmodl.ode)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
diff --git a/modules.html b/modules.html
index 0f1ffa99f8..3e7e03fa85 100644
--- a/modules.html
+++ b/modules.html
@@ -144,8 +144,8 @@ <h1>Python package<a class="headerlink" href="#python-package" title="Permalink
 <li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.differentiate2c"><code class="docutils literal notranslate"><span class="pre">differentiate2c()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.forwards_euler2c"><code class="docutils literal notranslate"><span class="pre">forwards_euler2c()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.integrate2c"><code class="docutils literal notranslate"><span class="pre">integrate2c()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.search_and_replace_protected_functions_from_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_functions_from_sympy()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.search_and_replace_protected_functions_to_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_functions_to_sympy()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_from_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_identifiers_from_sympy()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.search_and_replace_protected_identifiers_to_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_identifiers_to_sympy()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.solve_lin_system"><code class="docutils literal notranslate"><span class="pre">solve_lin_system()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="nmodl.html#nmodl.ode.solve_non_lin_system"><code class="docutils literal notranslate"><span class="pre">solve_non_lin_system()</span></code></a></li>
 </ul>
diff --git a/nmodl.html b/nmodl.html
index 275fb14754..555c17af96 100644
--- a/nmodl.html
+++ b/nmodl.html
@@ -109,8 +109,8 @@
 <li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.differentiate2c"><code class="docutils literal notranslate"><span class="pre">differentiate2c()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.forwards_euler2c"><code class="docutils literal notranslate"><span class="pre">forwards_euler2c()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.integrate2c"><code class="docutils literal notranslate"><span class="pre">integrate2c()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.search_and_replace_protected_functions_from_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_functions_from_sympy()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.search_and_replace_protected_functions_to_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_functions_to_sympy()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.search_and_replace_protected_identifiers_from_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_identifiers_from_sympy()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.search_and_replace_protected_identifiers_to_sympy"><code class="docutils literal notranslate"><span class="pre">search_and_replace_protected_identifiers_to_sympy()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.solve_lin_system"><code class="docutils literal notranslate"><span class="pre">solve_lin_system()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#nmodl.ode.solve_non_lin_system"><code class="docutils literal notranslate"><span class="pre">solve_non_lin_system()</span></code></a></li>
 </ul>
@@ -432,13 +432,13 @@ <h1>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </dd></dl>
 
 <dl class="py function">
-<dt class="sig sig-object py" id="nmodl.ode.search_and_replace_protected_functions_from_sympy">
-<span class="sig-prename descclassname"><span class="pre">nmodl.ode.</span></span><span class="sig-name descname"><span class="pre">search_and_replace_protected_functions_from_sympy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eqs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function_calls</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nmodl/ode.html#search_and_replace_protected_functions_from_sympy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#nmodl.ode.search_and_replace_protected_functions_from_sympy" title="Permalink to this definition"></a></dt>
+<dt class="sig sig-object py" id="nmodl.ode.search_and_replace_protected_identifiers_from_sympy">
+<span class="sig-prename descclassname"><span class="pre">nmodl.ode.</span></span><span class="sig-name descname"><span class="pre">search_and_replace_protected_identifiers_from_sympy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eqs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function_calls</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nmodl/ode.html#search_and_replace_protected_identifiers_from_sympy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#nmodl.ode.search_and_replace_protected_identifiers_from_sympy" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
-<dt class="sig sig-object py" id="nmodl.ode.search_and_replace_protected_functions_to_sympy">
-<span class="sig-prename descclassname"><span class="pre">nmodl.ode.</span></span><span class="sig-name descname"><span class="pre">search_and_replace_protected_functions_to_sympy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eqs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function_calls</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nmodl/ode.html#search_and_replace_protected_functions_to_sympy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#nmodl.ode.search_and_replace_protected_functions_to_sympy" title="Permalink to this definition"></a></dt>
+<dt class="sig sig-object py" id="nmodl.ode.search_and_replace_protected_identifiers_to_sympy">
+<span class="sig-prename descclassname"><span class="pre">nmodl.ode.</span></span><span class="sig-name descname"><span class="pre">search_and_replace_protected_identifiers_to_sympy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eqs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vars</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function_calls</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nmodl/ode.html#search_and_replace_protected_identifiers_to_sympy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#nmodl.ode.search_and_replace_protected_identifiers_to_sympy" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
diff --git a/notebooks/nmodl-kinetic-schemes.ipynb b/notebooks/nmodl-kinetic-schemes.ipynb
index 43c159f56d..810e29d749 100644
--- a/notebooks/nmodl-kinetic-schemes.ipynb
+++ b/notebooks/nmodl-kinetic-schemes.ipynb
@@ -152,10 +152,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:42.341608Z",
-     "iopub.status.busy": "2024-05-21T21:13:42.341046Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.695116Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.694318Z"
+     "iopub.execute_input": "2024-05-22T07:50:45.406523Z",
+     "iopub.status.busy": "2024-05-22T07:50:45.406326Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.720649Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.719916Z"
     }
    },
    "outputs": [],
@@ -169,10 +169,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.698497Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.698028Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.727127Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.726466Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.723788Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.723293Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.749705Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.749075Z"
     }
    },
    "outputs": [],
@@ -277,10 +277,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.730454Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.729977Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.734473Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.733773Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.752709Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.752323Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.756613Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.755982Z"
     }
    },
    "outputs": [
@@ -323,10 +323,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.765703Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.765384Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.769437Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.768783Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.786301Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.785801Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.789732Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.789080Z"
     }
    },
    "outputs": [
@@ -367,10 +367,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.772200Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.771744Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.775902Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.775213Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.792247Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.791955Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.795526Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.794891Z"
     },
     "scrolled": true
    },
@@ -412,10 +412,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.778536Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.778174Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.782009Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.781378Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.797912Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.797574Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.801378Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.800663Z"
     },
     "scrolled": true
    },
@@ -459,10 +459,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:43.784523Z",
-     "iopub.status.busy": "2024-05-21T21:13:43.784258Z",
-     "iopub.status.idle": "2024-05-21T21:13:43.788672Z",
-     "shell.execute_reply": "2024-05-21T21:13:43.788020Z"
+     "iopub.execute_input": "2024-05-22T07:50:46.803803Z",
+     "iopub.status.busy": "2024-05-22T07:50:46.803432Z",
+     "iopub.status.idle": "2024-05-22T07:50:46.807387Z",
+     "shell.execute_reply": "2024-05-22T07:50:46.806726Z"
     }
    },
    "outputs": [
diff --git a/notebooks/nmodl-python-tutorial.ipynb b/notebooks/nmodl-python-tutorial.ipynb
index ceb94c6573..561b865213 100644
--- a/notebooks/nmodl-python-tutorial.ipynb
+++ b/notebooks/nmodl-python-tutorial.ipynb
@@ -30,10 +30,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:48.840334Z",
-     "iopub.status.busy": "2024-05-21T21:13:48.840124Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.181825Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.181090Z"
+     "iopub.execute_input": "2024-05-22T07:50:55.048210Z",
+     "iopub.status.busy": "2024-05-22T07:50:55.048013Z",
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@@ -63,10 +63,10 @@
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@@ -86,10 +86,10 @@
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@@ -152,10 +152,10 @@
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    "outputs": [],
@@ -183,10 +183,10 @@
    "execution_count": 5,
    "metadata": {
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-     "iopub.execute_input": "2024-05-21T21:13:50.228989Z",
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-     "shell.execute_reply": "2024-05-21T21:13:50.231856Z"
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+     "shell.execute_reply": "2024-05-22T07:50:56.407814Z"
     }
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    "outputs": [
@@ -235,10 +235,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.234838Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.234639Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.238849Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.238331Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.410828Z",
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+     "iopub.status.idle": "2024-05-22T07:50:56.414602Z",
+     "shell.execute_reply": "2024-05-22T07:50:56.414102Z"
     }
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    "outputs": [],
@@ -260,10 +260,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.241092Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.240898Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.244853Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.244197Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.416968Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.419748Z"
     }
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    "outputs": [
@@ -297,10 +297,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.247453Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.247022Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.254240Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.253586Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.422704Z",
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+     "iopub.status.idle": "2024-05-22T07:50:56.429748Z",
+     "shell.execute_reply": "2024-05-22T07:50:56.429052Z"
     }
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    "outputs": [
@@ -365,10 +365,10 @@
    "execution_count": 9,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.256748Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.256451Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.260674Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.259989Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.432182Z",
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+     "iopub.status.idle": "2024-05-22T07:50:56.435951Z",
+     "shell.execute_reply": "2024-05-22T07:50:56.435318Z"
     }
    },
    "outputs": [
@@ -416,10 +416,10 @@
    "execution_count": 10,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.263369Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.263007Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.266171Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.265647Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.438188Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.440518Z"
     }
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    "outputs": [],
@@ -441,10 +441,10 @@
    "execution_count": 11,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.268583Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.268208Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.272235Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.271554Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.443362Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.446134Z"
     }
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    "outputs": [
@@ -510,10 +510,10 @@
    "execution_count": 12,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.274759Z",
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-     "shell.execute_reply": "2024-05-21T21:13:50.276984Z"
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     }
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    "outputs": [
@@ -548,10 +548,10 @@
    "execution_count": 13,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.280065Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.279699Z",
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-     "shell.execute_reply": "2024-05-21T21:13:50.282734Z"
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     }
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    "outputs": [
@@ -584,10 +584,10 @@
    "execution_count": 14,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.285872Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.285506Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.288964Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.288316Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.460087Z",
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     }
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    "outputs": [
@@ -622,10 +622,10 @@
    "execution_count": 15,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.291466Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.291082Z",
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-     "shell.execute_reply": "2024-05-21T21:13:50.294686Z"
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+     "shell.execute_reply": "2024-05-22T07:50:56.469689Z"
     }
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    "outputs": [
@@ -669,10 +669,10 @@
    "execution_count": 16,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.297617Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.297419Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.303009Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.302364Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.472486Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.477234Z"
     }
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    "outputs": [
@@ -733,10 +733,10 @@
    "execution_count": 17,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.305281Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.305088Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.308660Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.308007Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.480377Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.482760Z"
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    "outputs": [],
@@ -761,10 +761,10 @@
    "execution_count": 18,
    "metadata": {
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-     "iopub.execute_input": "2024-05-21T21:13:50.311070Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.310619Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.320781Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.320232Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.485889Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.495144Z"
     }
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    "outputs": [],
@@ -857,10 +857,10 @@
    "execution_count": 19,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.322948Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.322757Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.326212Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.325566Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.497908Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.500699Z"
     }
    },
    "outputs": [
@@ -897,10 +897,10 @@
    "execution_count": 20,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:50.328608Z",
-     "iopub.status.busy": "2024-05-21T21:13:50.328411Z",
-     "iopub.status.idle": "2024-05-21T21:13:50.333717Z",
-     "shell.execute_reply": "2024-05-21T21:13:50.333071Z"
+     "iopub.execute_input": "2024-05-22T07:50:56.503894Z",
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+     "shell.execute_reply": "2024-05-22T07:50:56.508447Z"
     }
    },
    "outputs": [
diff --git a/notebooks/nmodl-sympy-conductance.ipynb b/notebooks/nmodl-sympy-conductance.ipynb
index 63d6968f17..da91eecd2c 100644
--- a/notebooks/nmodl-sympy-conductance.ipynb
+++ b/notebooks/nmodl-sympy-conductance.ipynb
@@ -86,10 +86,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:52.703914Z",
-     "iopub.status.busy": "2024-05-21T21:13:52.703434Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.051167Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.050468Z"
+     "iopub.execute_input": "2024-05-22T07:50:58.605653Z",
+     "iopub.status.busy": "2024-05-22T07:50:58.605441Z",
+     "iopub.status.idle": "2024-05-22T07:50:59.925217Z",
+     "shell.execute_reply": "2024-05-22T07:50:59.924457Z"
     }
    },
    "outputs": [],
@@ -103,10 +103,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.054259Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.053932Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.081127Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.080493Z"
+     "iopub.execute_input": "2024-05-22T07:50:59.928093Z",
+     "iopub.status.busy": "2024-05-22T07:50:59.927880Z",
+     "iopub.status.idle": "2024-05-22T07:50:59.954361Z",
+     "shell.execute_reply": "2024-05-22T07:50:59.953751Z"
     }
    },
    "outputs": [],
@@ -149,10 +149,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.084215Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.083880Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.361546Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.360852Z"
+     "iopub.execute_input": "2024-05-22T07:50:59.956896Z",
+     "iopub.status.busy": "2024-05-22T07:50:59.956688Z",
+     "iopub.status.idle": "2024-05-22T07:51:00.216116Z",
+     "shell.execute_reply": "2024-05-22T07:51:00.215376Z"
     }
    },
    "outputs": [
@@ -196,10 +196,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.364402Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.363983Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.513534Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.512840Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.219133Z",
+     "iopub.status.busy": "2024-05-22T07:51:00.218712Z",
+     "iopub.status.idle": "2024-05-22T07:51:00.362942Z",
+     "shell.execute_reply": "2024-05-22T07:51:00.362251Z"
     }
    },
    "outputs": [
@@ -243,10 +243,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.516351Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.515897Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.522655Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.521906Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.365770Z",
+     "iopub.status.busy": "2024-05-22T07:51:00.365498Z",
+     "iopub.status.idle": "2024-05-22T07:51:00.371677Z",
+     "shell.execute_reply": "2024-05-22T07:51:00.371000Z"
     }
    },
    "outputs": [
@@ -290,10 +290,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.525428Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.524986Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.541643Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.541015Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.373961Z",
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+     "shell.execute_reply": "2024-05-22T07:51:00.388743Z"
     }
    },
    "outputs": [
@@ -337,10 +337,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.544187Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.543953Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.666680Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.666009Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.391743Z",
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     }
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    "outputs": [
@@ -400,10 +400,10 @@
    "execution_count": 8,
    "metadata": {
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-     "shell.execute_reply": "2024-05-21T21:13:54.771689Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.512169Z",
+     "iopub.status.busy": "2024-05-22T07:51:00.511727Z",
+     "iopub.status.idle": "2024-05-22T07:51:00.610866Z",
+     "shell.execute_reply": "2024-05-22T07:51:00.610236Z"
     }
    },
    "outputs": [
@@ -456,10 +456,10 @@
    "execution_count": 9,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:54.774979Z",
-     "iopub.status.busy": "2024-05-21T21:13:54.774755Z",
-     "iopub.status.idle": "2024-05-21T21:13:54.848573Z",
-     "shell.execute_reply": "2024-05-21T21:13:54.847889Z"
+     "iopub.execute_input": "2024-05-22T07:51:00.613500Z",
+     "iopub.status.busy": "2024-05-22T07:51:00.613263Z",
+     "iopub.status.idle": "2024-05-22T07:51:00.685150Z",
+     "shell.execute_reply": "2024-05-22T07:51:00.684420Z"
     }
    },
    "outputs": [
diff --git a/notebooks/nmodl-sympy-solver-cnexp.ipynb b/notebooks/nmodl-sympy-solver-cnexp.ipynb
index 614e432167..424e177840 100644
--- a/notebooks/nmodl-sympy-solver-cnexp.ipynb
+++ b/notebooks/nmodl-sympy-solver-cnexp.ipynb
@@ -62,10 +62,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:56.713483Z",
-     "iopub.status.busy": "2024-05-21T21:13:56.713286Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.045336Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.044630Z"
+     "iopub.execute_input": "2024-05-22T07:51:02.331013Z",
+     "iopub.status.busy": "2024-05-22T07:51:02.330359Z",
+     "iopub.status.idle": "2024-05-22T07:51:03.646550Z",
+     "shell.execute_reply": "2024-05-22T07:51:03.645822Z"
     }
    },
    "outputs": [],
@@ -79,10 +79,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.048672Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.048281Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.076145Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.075220Z"
+     "iopub.execute_input": "2024-05-22T07:51:03.649688Z",
+     "iopub.status.busy": "2024-05-22T07:51:03.649293Z",
+     "iopub.status.idle": "2024-05-22T07:51:03.675736Z",
+     "shell.execute_reply": "2024-05-22T07:51:03.675098Z"
     }
    },
    "outputs": [],
@@ -123,10 +123,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.079692Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.079187Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.503645Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.502915Z"
+     "iopub.execute_input": "2024-05-22T07:51:03.678502Z",
+     "iopub.status.busy": "2024-05-22T07:51:03.678258Z",
+     "iopub.status.idle": "2024-05-22T07:51:04.102115Z",
+     "shell.execute_reply": "2024-05-22T07:51:04.101410Z"
     }
    },
    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.506498Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.505978Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.636725Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.635986Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.104749Z",
+     "iopub.status.busy": "2024-05-22T07:51:04.104518Z",
+     "iopub.status.idle": "2024-05-22T07:51:04.233810Z",
+     "shell.execute_reply": "2024-05-22T07:51:04.233059Z"
     }
    },
    "outputs": [
@@ -207,10 +207,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.639552Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.639091Z",
-     "iopub.status.idle": "2024-05-21T21:13:58.869674Z",
-     "shell.execute_reply": "2024-05-21T21:13:58.868909Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.236684Z",
+     "iopub.status.busy": "2024-05-22T07:51:04.236270Z",
+     "iopub.status.idle": "2024-05-22T07:51:04.466415Z",
+     "shell.execute_reply": "2024-05-22T07:51:04.465692Z"
     }
    },
    "outputs": [
@@ -218,7 +218,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "exact solution:\t     m = minf-(-m+minf)*exp(-dt/mtau)\n"
+      "exact solution:\t"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "     m = minf-(-m+minf)*exp(-dt/mtau)\n"
      ]
     },
     {
@@ -255,10 +262,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:58.872589Z",
-     "iopub.status.busy": "2024-05-21T21:13:58.872344Z",
-     "iopub.status.idle": "2024-05-21T21:13:59.062127Z",
-     "shell.execute_reply": "2024-05-21T21:13:59.061441Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.469423Z",
+     "iopub.status.busy": "2024-05-22T07:51:04.468973Z",
+     "iopub.status.idle": "2024-05-22T07:51:04.658425Z",
+     "shell.execute_reply": "2024-05-22T07:51:04.657708Z"
     }
    },
    "outputs": [
@@ -266,7 +273,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "exact solution:\t     m = minf+(m-minf)*exp(dt/mtau)\n",
+      "exact solution:\t     m = minf+(m-minf)*exp(dt/mtau)\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "pade approx:\t     m = (-dt*m+2.0*dt*minf-2.0*m*mtau)/(dt-2.0*mtau)\n"
      ]
     }
@@ -297,10 +310,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:13:59.064836Z",
-     "iopub.status.busy": "2024-05-21T21:13:59.064376Z",
-     "iopub.status.idle": "2024-05-21T21:14:00.452222Z",
-     "shell.execute_reply": "2024-05-21T21:14:00.451520Z"
+     "iopub.execute_input": "2024-05-22T07:51:04.661370Z",
+     "iopub.status.busy": "2024-05-22T07:51:04.660943Z",
+     "iopub.status.idle": "2024-05-22T07:51:06.047306Z",
+     "shell.execute_reply": "2024-05-22T07:51:06.046692Z"
     }
    },
    "outputs": [
@@ -345,10 +358,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:00.454829Z",
-     "iopub.status.busy": "2024-05-21T21:14:00.454433Z",
-     "iopub.status.idle": "2024-05-21T21:14:02.255109Z",
-     "shell.execute_reply": "2024-05-21T21:14:02.254377Z"
+     "iopub.execute_input": "2024-05-22T07:51:06.049973Z",
+     "iopub.status.busy": "2024-05-22T07:51:06.049557Z",
+     "iopub.status.idle": "2024-05-22T07:51:07.832398Z",
+     "shell.execute_reply": "2024-05-22T07:51:07.831659Z"
     }
    },
    "outputs": [
diff --git a/notebooks/nmodl-sympy-solver-derivimplicit.ipynb b/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
index de660565d2..ceda497eef 100644
--- a/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
+++ b/notebooks/nmodl-sympy-solver-derivimplicit.ipynb
@@ -39,10 +39,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:03.901559Z",
-     "iopub.status.busy": "2024-05-21T21:14:03.901362Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.216294Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.215535Z"
+     "iopub.execute_input": "2024-05-22T07:51:09.398526Z",
+     "iopub.status.busy": "2024-05-22T07:51:09.398326Z",
+     "iopub.status.idle": "2024-05-22T07:51:10.733117Z",
+     "shell.execute_reply": "2024-05-22T07:51:10.732364Z"
     }
    },
    "outputs": [],
@@ -56,10 +56,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.219326Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.219069Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.246901Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.246266Z"
+     "iopub.execute_input": "2024-05-22T07:51:10.736274Z",
+     "iopub.status.busy": "2024-05-22T07:51:10.735844Z",
+     "iopub.status.idle": "2024-05-22T07:51:10.764120Z",
+     "shell.execute_reply": "2024-05-22T07:51:10.763477Z"
     }
    },
    "outputs": [],
@@ -100,10 +100,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.250032Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.249553Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.712690Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.712004Z"
+     "iopub.execute_input": "2024-05-22T07:51:10.767000Z",
+     "iopub.status.busy": "2024-05-22T07:51:10.766771Z",
+     "iopub.status.idle": "2024-05-22T07:51:11.233306Z",
+     "shell.execute_reply": "2024-05-22T07:51:11.232563Z"
     }
    },
    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:05.715287Z",
-     "iopub.status.busy": "2024-05-21T21:14:05.715034Z",
-     "iopub.status.idle": "2024-05-21T21:14:05.924246Z",
-     "shell.execute_reply": "2024-05-21T21:14:05.923582Z"
+     "iopub.execute_input": "2024-05-22T07:51:11.235831Z",
+     "iopub.status.busy": "2024-05-22T07:51:11.235569Z",
+     "iopub.status.idle": "2024-05-22T07:51:11.447741Z",
+     "shell.execute_reply": "2024-05-22T07:51:11.447008Z"
     }
    },
    "outputs": [
diff --git a/notebooks/nmodl-sympy-solver-sparse.ipynb b/notebooks/nmodl-sympy-solver-sparse.ipynb
index e23506ee2a..3dec84bbbc 100644
--- a/notebooks/nmodl-sympy-solver-sparse.ipynb
+++ b/notebooks/nmodl-sympy-solver-sparse.ipynb
@@ -39,10 +39,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:07.178173Z",
-     "iopub.status.busy": "2024-05-21T21:14:07.177713Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.484640Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.483861Z"
+     "iopub.execute_input": "2024-05-22T07:51:12.891134Z",
+     "iopub.status.busy": "2024-05-22T07:51:12.890591Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.214689Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.213944Z"
     }
    },
    "outputs": [],
@@ -56,10 +56,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.488009Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.487560Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.514113Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.513543Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.217973Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.217528Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.243870Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.243286Z"
     }
    },
    "outputs": [],
@@ -100,10 +100,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.516782Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.516468Z",
-     "iopub.status.idle": "2024-05-21T21:14:08.980321Z",
-     "shell.execute_reply": "2024-05-21T21:14:08.979573Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.246960Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.246408Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.710041Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.709339Z"
     }
    },
    "outputs": [
@@ -165,10 +165,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-05-21T21:14:08.983046Z",
-     "iopub.status.busy": "2024-05-21T21:14:08.982759Z",
-     "iopub.status.idle": "2024-05-21T21:14:09.200346Z",
-     "shell.execute_reply": "2024-05-21T21:14:09.199627Z"
+     "iopub.execute_input": "2024-05-22T07:51:14.713086Z",
+     "iopub.status.busy": "2024-05-22T07:51:14.712493Z",
+     "iopub.status.idle": "2024-05-22T07:51:14.923334Z",
+     "shell.execute_reply": "2024-05-22T07:51:14.922620Z"
     }
    },
    "outputs": [
diff --git a/objects.inv b/objects.inv
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GIT binary patch
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"Ex.-4"]], "Ex. 5": [[14, "Ex.-5"], [19, "Ex.-5"], [20, "Ex.-5"]], "NMODL LINEAR solver": [[15, "NMODL-LINEAR-solver"]], "NMODL NONLINEAR solver": [[16, "NMODL-NONLINEAR-solver"]], "Newton solver": [[16, "Newton-solver"]], "Fall-back solver": [[16, "Fall-back-solver"]], "NMODL integration of ODEs": [[17, "NMODL-integration-of-ODEs"]], "KINETIC block": [[17, "KINETIC-block"]], "DERIVATIVE block": [[17, "DERIVATIVE-block"]], "LINEAR block": [[17, "LINEAR-block"]], "NONLINEAR block": [[17, "NONLINEAR-block"]], "NMODL Python Interface Tutorial": [[18, "NMODL-Python-Interface-Tutorial"]], "Introduction": [[18, "Introduction"], [19, "Introduction"], [23, "introduction"]], "Parsing Model And Constructing AST": [[18, "Parsing-Model-And-Constructing-AST"]], "Querying AST object with Visitors": [[18, "Querying-AST-object-with-Visitors"]], "Lookup visitor": [[18, "Lookup-visitor"]], "Custom AST visitor": [[18, "Custom-AST-visitor"]], "Easy code generation using AST visitors": [[18, "Easy-code-generation-using-AST-visitors"]], "Example of CURIE information parsing": [[18, "Example-of-CURIE-information-parsing"]], "NMODL CONDUCTANCE": [[19, "NMODL-CONDUCTANCE"]], "Implementation": [[19, "Implementation"], [20, "Implementation"], [21, "Implementation"], [22, "Implementation"]], "Implementation Tests": [[19, "Implementation-Tests"], [20, "Implementation-Tests"], [21, "Implementation-Tests"], [22, "Implementation-Tests"]], "Ex. 6": [[19, "Ex.-6"], [20, "Ex.-6"]], "Ex. 7": [[19, "Ex.-7"]], "NMODL SympySolver - cnexp": [[20, "NMODL-SympySolver---cnexp"]], "Pade approximant": [[20, "Pade-approximant"]], "NMODL SympySolver - derivimplicit": [[21, "NMODL-SympySolver---derivimplicit"]], "NMODL SympySolver - sparse": [[22, "NMODL-SympySolver---sparse"]], "The NMODL Framework": [[23, "the-nmodl-framework"]], "Installation": [[23, "installation"]], "Try NMODL with Docker": [[23, "try-nmodl-with-docker"]], "Using the Python API": [[23, "using-the-python-api"]], "High Level Analysis and Code Generation": [[23, "high-level-analysis-and-code-generation"]], "Documentation": [[23, "documentation"]], "Citation": [[23, "citation"]], "Support / Contribuition": [[23, "support-contribuition"]], "Examples / Benchmarks": [[23, "examples-benchmarks"]], "Funding & Acknowledgment": [[23, "funding-acknowledgment"]]}, "indexentries": {"nmodldriver (class in nmodl)": [[11, "nmodl.NmodlDriver"]], "differentiate2c() (in module nmodl.ode)": [[11, "nmodl.ode.differentiate2c"]], "forwards_euler2c() (in module nmodl.ode)": [[11, "nmodl.ode.forwards_euler2c"]], "get_ast() (nmodl.nmodldriver method)": [[11, "nmodl.NmodlDriver.get_ast"]], "integrate2c() (in module nmodl.ode)": [[11, "nmodl.ode.integrate2c"]], "list_examples() (in module nmodl.dsl)": [[11, "nmodl.dsl.list_examples"]], "load_example() (in module nmodl.dsl)": [[11, "nmodl.dsl.load_example"]], "module": [[11, "module-nmodl"], [11, "module-nmodl.ast"], [11, "module-nmodl.dsl"], [11, "module-nmodl.ode"], [11, "module-nmodl.symtab"], [11, "module-nmodl.visitor"]], "nmodl": [[11, "module-nmodl"]], "nmodl.ast": [[11, "module-nmodl.ast"]], "nmodl.dsl": [[11, "module-nmodl.dsl"]], "nmodl.ode": [[11, "module-nmodl.ode"]], "nmodl.symtab": [[11, "module-nmodl.symtab"]], "nmodl.visitor": [[11, "module-nmodl.visitor"]], "parse_file() (nmodl.nmodldriver method)": [[11, "nmodl.NmodlDriver.parse_file"]], "parse_stream() (nmodl.nmodldriver method)": [[11, "nmodl.NmodlDriver.parse_stream"]], "parse_string() (nmodl.nmodldriver method)": [[11, "nmodl.NmodlDriver.parse_string"]], "search_and_replace_protected_identifiers_from_sympy() (in module nmodl.ode)": [[11, "nmodl.ode.search_and_replace_protected_identifiers_from_sympy"]], "search_and_replace_protected_identifiers_to_sympy() (in module nmodl.ode)": [[11, "nmodl.ode.search_and_replace_protected_identifiers_to_sympy"]], "solve_lin_system() (in module nmodl.ode)": [[11, "nmodl.ode.solve_lin_system"]], "solve_non_lin_system() (in module nmodl.ode)": [[11, "nmodl.ode.solve_non_lin_system"]], "to_json() (in module nmodl)": [[11, "nmodl.to_json"]], "to_nmodl() (in module nmodl)": [[11, "nmodl.to_nmodl"]], "view() (in module nmodl.ast)": [[11, "nmodl.ast.view"]]}})
\ No newline at end of file