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update ipynb to more modern Python + NEURON style #3357

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fa8b7d2
update ipynb to more modern Python + NEURON style
ramcdougal Mar 21, 2025
e007158
fixed files that were missed due to spaces in filename
ramcdougal Mar 21, 2025
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38 changes: 18 additions & 20 deletions docs/nmodl/transpiler/notebooks/nmodl-python-tutorial.ipynb
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Expand Up @@ -152,7 +152,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -164,7 +164,7 @@
}
],
"source": [
"print(\"%.200s\" % modast) # only first 200 characters"
"print(f\"{modast:.200s}\") # only first 200 characters"
]
},
{
Expand Down Expand Up @@ -235,7 +235,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -259,32 +259,33 @@
"units = lookup_visitor.lookup(modast, ast.AstNodeType.UNIT)\n",
"\n",
"if odes:\n",
" print(\"%d differential equation(s) exist : \" % len(odes))\n",
" print(f\"{len(odes)} differential equation(s) exist:\")\n",
" for ode in odes:\n",
" print(\"\\t %s \" % nmodl.to_nmodl(ode))\n",
" print(f\"\\t {nmodl.to_nmodl(ode)}\")\n",
"\n",
"if primes:\n",
" print(\"%d prime variables exist :\" % len(primes), end=\"\")\n",
" print(f\"{len(primes)} prime variables exist:\", end=\"\")\n",
" for prime in primes:\n",
" print(\" %s\" % nmodl.to_nmodl(prime), end=\"\")\n",
" print(f\" {nmodl.to_nmodl(prime)}\", end=\"\")\n",
" print()\n",
"\n",
"if range_vars:\n",
" print(\"%d range variables exist :\" % len(range_vars), end=\"\")\n",
" print(f\"{len(range_vars)} range variables exist:\", end=\"\")\n",
" for range_var in range_vars:\n",
" print(\" %s\" % nmodl.to_nmodl(range_var), end=\"\")\n",
" print(f\" {nmodl.to_nmodl(range_var)}\", end=\"\")\n",
" print()\n",
"\n",
"if parameters:\n",
" print(\"%d parameter variables exist :\" % len(parameters), end=\"\")\n",
" for range_var in range_vars:\n",
" print(\" %s\" % nmodl.to_nmodl(range_var), end=\"\")\n",
" print(f\"{len(parameters)} parameter variables exist:\", end=\"\")\n",
" for parameter in parameters:\n",
" print(f\" {nmodl.to_nmodl(parameter)}\", end=\"\")\n",
" print()\n",
"\n",
"if units:\n",
" print(\"%d units uses :\" % len(units), end=\"\")\n",
" print(f\"{len(units)} units uses:\", end=\"\")\n",
" for unit in units:\n",
" print(\" %s\" % nmodl.to_nmodl(unit), end=\"\")"
" print(f\" {nmodl.to_nmodl(unit)}\", end=\"\")\n",
" print()"
]
},
{
Expand Down Expand Up @@ -747,7 +748,7 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -782,15 +783,12 @@
"\n",
"ont_statements = lookup_visitor.lookup(modast, ast.AstNodeType.ONTOLOGY_STATEMENT)\n",
"ions = lookup_visitor.lookup(modast, ast.AstNodeType.USEION)\n",
"\n",
"for statement in ont_statements:\n",
" print(\n",
" \" %s (%s)\" % (nmodl.to_nmodl(statement), nmodl.to_nmodl(statement.ontology_id))\n",
" )\n",
" print(f\" {nmodl.to_nmodl(statement)} ({nmodl.to_nmodl(statement.ontology_id)})\")\n",
"\n",
"for ion in ions:\n",
" o_id = nmodl.to_nmodl(ion.ontology_id) if ion.ontology_id else \"\"\n",
" print(\" %s (%s)\" % (nmodl.to_nmodl(ion), o_id))"
" print(f\" {nmodl.to_nmodl(ion)} ({o_id})\")\n"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion docs/rxd-tutorials/Changing initial conditions and parameters.ipynb
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Expand Up @@ -64,7 +64,7 @@
"\n",
"h.load_file(\"stdrun.hoc\")\n",
"\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"cyt = rxd.Region([soma], name=\"cyt\", nrn_region=\"i\")\n",
"u = rxd.Species(cyt, name=\"u\")\n",
"α = rxd.Parameter(cyt, value=0.3 * mM)\n",
Expand Down
6 changes: 3 additions & 3 deletions docs/rxd-tutorials/Restricting reactions to certain sections.ipynb
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Expand Up @@ -89,8 +89,8 @@
"metadata": {},
"outputs": [],
"source": [
"left = h.Section(name=\"left\")\n",
"right = h.Section(name=\"right\")\n",
"left = h.Section(\"left\")\n",
"right = h.Section(\"right\")\n",
"\n",
"left.nseg = right.nseg = 101\n",
"left.L = right.L = 101\n",
Expand Down Expand Up @@ -271,7 +271,7 @@
"def plot(fig):\n",
" y = protein.nodes.concentration\n",
" x = [h.distance(node, left(0)) for node in protein.nodes]\n",
" fig.add_trace(go.Scatter(x=x, y=y, name=f\"t = {h.t:g} ms\"))"
" fig.add_trace(go.Scatter(x=x, y=y, name=f\"t = {h.t} ms\"))"
]
},
{
Expand Down
6 changes: 3 additions & 3 deletions docs/rxd-tutorials/basic-initialization.ipynb
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Expand Up @@ -44,7 +44,7 @@
"from neuron import h, rxd\n",
"from neuron.units import mV\n",
"\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"cyt = rxd.Region(soma.wholetree(), name=\"cyt\", nrn_region=\"i\")\n",
"\n",
"ca = rxd.Species(cyt, name=\"ca\", charge=2, atolscale=1e-6)\n",
Expand Down Expand Up @@ -90,7 +90,7 @@
"from neuron import h, rxd\n",
"from neuron.units import mV\n",
"\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"cyt = rxd.Region(soma.wholetree(), name=\"cyt\")\n",
"\n",
"ca = rxd.Species(cyt, name=\"ca\", charge=2)\n",
Expand Down Expand Up @@ -187,7 +187,7 @@
"from neuron import h, rxd\n",
"from neuron.units import mV\n",
"\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"\n",
"cyt = rxd.Region([soma], name=\"cyt\")\n",
"m = rxd.State(cyt, initial=0.47)\n",
Expand Down
10 changes: 5 additions & 5 deletions docs/rxd-tutorials/calcium waves.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@
"metadata": {},
"outputs": [],
"source": [
"sec = h.Section(name=\"sec\")\n",
"sec = h.Section(\"sec\")\n",
"sec.L = 101\n",
"sec.diam = 1\n",
"sec.nseg = 101"
Expand Down Expand Up @@ -181,7 +181,7 @@
"outputs": [],
"source": [
"cyt = rxd.Region(\n",
" h.allsec(),\n",
" [sec],\n",
" nrn_region=\"i\",\n",
" geometry=rxd.FractionalVolume(fc, surface_fraction=1),\n",
" name=\"cyt\",\n",
Expand Down Expand Up @@ -211,7 +211,7 @@
"metadata": {},
"outputs": [],
"source": [
"er = rxd.Region(h.allsec(), geometry=rxd.FractionalVolume(fe), name=\"er\")"
"er = rxd.Region([sec], geometry=rxd.FractionalVolume(fe), name=\"er\")"
]
},
{
Expand All @@ -228,7 +228,7 @@
"outputs": [],
"source": [
"cyt_er_membrane = rxd.Region(\n",
" h.allsec(), geometry=rxd.DistributedBoundary(2), name=\"cyt_er_membrane\"\n",
" [sec], geometry=rxd.DistributedBoundary(2), name=\"cyt_er_membrane\"\n",
")"
]
},
Expand Down Expand Up @@ -273,7 +273,7 @@
" <li><code>name</code> assigns a name to the Species that syncs with the rest of NEURON (NMODL, GUI tools, variables of the form e.g. <code>cai</code>, etc)</li>\n",
" <li><code>charge</code> refers to the charge of the Species; e.g. a calcium ion would have charge 2</li>\n",
" <li><code>initial</code> refers to the initial concentration of the Species. If <code>initial</code> is not specified and the Species has a name and exists on an rxd.Region with <code>nrn_region</code> set, then NEURON's default initialization rules apply; otherwise the default is 0.</li>\n",
" <li><code>atolscale</code> indicates a tolerance scale factor for variable step integration and is especially important for calcium and other substances with a low concentration</li>\n",
" <li><code>atolscale</code> indicates a tolerance scale factor for variable step integration and is especially important for calcium and other substances with a low concentration. (For calcium, consider an atolscale around 1e-6.)</li>\n",
"</ul>"
]
},
Expand Down
2 changes: 1 addition & 1 deletion docs/rxd-tutorials/circadian.ipynb
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Expand Up @@ -155,7 +155,7 @@
"metadata": {},
"outputs": [],
"source": [
"cell = h.Section(name=\"cell\")\n",
"cell = h.Section(\"cell\")\n",
"cell.diam = cell.L = 5\n",
"r = rxd.Region([cell], nrn_region=\"i\")"
]
Expand Down
2 changes: 1 addition & 1 deletion docs/rxd-tutorials/combining currents from mod files with rxd.ipynb
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Expand Up @@ -95,7 +95,7 @@
"outputs": [],
"source": [
"## define morphology\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"soma.L = soma.diam = 10 * um\n",
"\n",
"## add ion channels (h.hh is built in, so always available)\n",
Expand Down
8 changes: 4 additions & 4 deletions docs/rxd-tutorials/ip3-demo.ipynb
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Expand Up @@ -24,7 +24,7 @@
"metadata": {},
"outputs": [],
"source": [
"dend = h.Section(name=\"dend\")\n",
"dend = h.Section(\"dend\")\n",
"dend.L = 100\n",
"dend.nseg = 101"
]
Expand Down Expand Up @@ -88,7 +88,7 @@
"while dend(0.7).ip3i < 100 * nM:\n",
" h.fadvance()\n",
"\n",
"print(\"crossed 100 nM at t = {} ms\".format(h.t))"
"print(f\"crossed 100 nM at t = {h.t} ms\")"
]
},
{
Expand All @@ -105,8 +105,8 @@
"h.finitialize(-65)\n",
"h.continuerun(1000)\n",
"max_ip3 = max(ip3_vec)\n",
"print(\"peak ip3 =\", max_ip3)\n",
"print(\"final ip3 =\", dend(0.7).ip3i)"
"print(f\"peak ip3 = {max_ip3}\")\n",
"print(f\"final ip3 = {dend(0.7).ip3i}\")"
]
}
],
Expand Down
12 changes: 6 additions & 6 deletions docs/rxd-tutorials/thresholds.ipynb
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Expand Up @@ -29,10 +29,10 @@
"outputs": [],
"source": [
"from matplotlib import pyplot as plt\n",
"import numpy\n",
"import numpy as np\n",
"\n",
"x = numpy.linspace(-5, 5)\n",
"y = numpy.tanh(x)\n",
"x = np.linspace(-5, 5)\n",
"y = np.tanh(x)\n",
"plt.grid()\n",
"plt.plot(x, y)\n",
"plt.xlabel(\"x\")\n",
Expand Down Expand Up @@ -78,8 +78,8 @@
"metadata": {},
"outputs": [],
"source": [
"x = numpy.linspace(0, 4, 1000)\n",
"y = (1 + numpy.tanh(2 * 10 * (x - 2))) / 2\n",
"x = np.linspace(0, 4, 1000)\n",
"y = (1 + np.tanh(2 * 10 * (x - 2))) / 2\n",
"plt.grid()\n",
"plt.plot(x, y)\n",
"plt.xlabel(\"x\")\n",
Expand Down Expand Up @@ -113,7 +113,7 @@
"\n",
"h.load_file(\"stdrun.hoc\")\n",
"\n",
"soma = h.Section(name=\"soma\")\n",
"soma = h.Section(\"soma\")\n",
"cyt = rxd.Region([soma], name=\"cyt\", nrn_region=\"i\")\n",
"ip3 = rxd.Species(cyt, name=\"ip3\", charge=0, initial=1 * mM)\n",
"k = 2 # degradation rate\n",
Expand Down
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