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b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb index f77d90137..e314791b0 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb @@ -152,10 +152,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:28.231435Z", - "iopub.status.busy": "2024-10-01T10:21:28.231238Z", - "iopub.status.idle": "2024-10-01T10:21:29.033845Z", - "shell.execute_reply": "2024-10-01T10:21:29.033024Z" + "iopub.execute_input": "2024-10-03T09:53:27.189915Z", + "iopub.status.busy": "2024-10-03T09:53:27.189431Z", + "iopub.status.idle": "2024-10-03T09:53:27.978488Z", + "shell.execute_reply": "2024-10-03T09:53:27.977663Z" } }, "outputs": [], @@ -169,10 +169,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.036443Z", - "iopub.status.busy": "2024-10-01T10:21:29.036030Z", - "iopub.status.idle": "2024-10-01T10:21:29.066797Z", - "shell.execute_reply": "2024-10-01T10:21:29.066164Z" + "iopub.execute_input": "2024-10-03T09:53:27.981149Z", + "iopub.status.busy": "2024-10-03T09:53:27.980922Z", + "iopub.status.idle": "2024-10-03T09:53:28.011658Z", + "shell.execute_reply": "2024-10-03T09:53:28.011033Z" } }, "outputs": [], @@ -277,10 +277,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.069059Z", - "iopub.status.busy": "2024-10-01T10:21:29.068722Z", - "iopub.status.idle": "2024-10-01T10:21:29.073735Z", - "shell.execute_reply": "2024-10-01T10:21:29.073036Z" + "iopub.execute_input": "2024-10-03T09:53:28.014217Z", + "iopub.status.busy": "2024-10-03T09:53:28.013738Z", + "iopub.status.idle": "2024-10-03T09:53:28.018271Z", + "shell.execute_reply": "2024-10-03T09:53:28.017636Z" } }, "outputs": [ @@ -323,10 +323,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.103779Z", - "iopub.status.busy": "2024-10-01T10:21:29.103327Z", - "iopub.status.idle": "2024-10-01T10:21:29.107488Z", - "shell.execute_reply": "2024-10-01T10:21:29.106918Z" + "iopub.execute_input": "2024-10-03T09:53:28.048586Z", + "iopub.status.busy": "2024-10-03T09:53:28.048123Z", + "iopub.status.idle": "2024-10-03T09:53:28.051868Z", + "shell.execute_reply": "2024-10-03T09:53:28.051320Z" } }, "outputs": [ @@ -367,10 +367,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.109512Z", - "iopub.status.busy": "2024-10-01T10:21:29.109150Z", - "iopub.status.idle": "2024-10-01T10:21:29.112981Z", - "shell.execute_reply": "2024-10-01T10:21:29.112414Z" + "iopub.execute_input": "2024-10-03T09:53:28.054128Z", + "iopub.status.busy": "2024-10-03T09:53:28.053610Z", + "iopub.status.idle": "2024-10-03T09:53:28.057453Z", + "shell.execute_reply": "2024-10-03T09:53:28.056897Z" }, "scrolled": true }, @@ -412,10 +412,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.114916Z", - "iopub.status.busy": "2024-10-01T10:21:29.114547Z", - "iopub.status.idle": "2024-10-01T10:21:29.118506Z", - "shell.execute_reply": "2024-10-01T10:21:29.117935Z" + "iopub.execute_input": "2024-10-03T09:53:28.059453Z", + "iopub.status.busy": "2024-10-03T09:53:28.059082Z", + "iopub.status.idle": "2024-10-03T09:53:28.062912Z", + "shell.execute_reply": "2024-10-03T09:53:28.062353Z" }, "scrolled": true }, @@ -459,10 +459,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.120491Z", - "iopub.status.busy": "2024-10-01T10:21:29.120121Z", - "iopub.status.idle": "2024-10-01T10:21:29.124711Z", - "shell.execute_reply": "2024-10-01T10:21:29.124162Z" + "iopub.execute_input": "2024-10-03T09:53:28.064721Z", + "iopub.status.busy": "2024-10-03T09:53:28.064520Z", + "iopub.status.idle": "2024-10-03T09:53:28.069195Z", + "shell.execute_reply": "2024-10-03T09:53:28.068634Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb index 8bf04d8fc..adf221707 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb @@ -30,10 +30,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:34.429599Z", - "iopub.status.busy": "2024-10-01T10:21:34.429205Z", - "iopub.status.idle": "2024-10-01T10:21:35.235253Z", - "shell.execute_reply": "2024-10-01T10:21:35.234452Z" + "iopub.execute_input": "2024-10-03T09:53:33.628062Z", + "iopub.status.busy": "2024-10-03T09:53:33.627869Z", + "iopub.status.idle": "2024-10-03T09:53:34.423988Z", + "shell.execute_reply": "2024-10-03T09:53:34.423097Z" } }, "outputs": [], @@ -63,10 +63,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.237787Z", - "iopub.status.busy": "2024-10-01T10:21:35.237566Z", - "iopub.status.idle": "2024-10-01T10:21:35.267042Z", - "shell.execute_reply": "2024-10-01T10:21:35.266427Z" + "iopub.execute_input": "2024-10-03T09:53:34.426837Z", + "iopub.status.busy": "2024-10-03T09:53:34.426419Z", + "iopub.status.idle": "2024-10-03T09:53:34.455042Z", + "shell.execute_reply": "2024-10-03T09:53:34.454411Z" } }, "outputs": [], @@ -86,10 +86,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.269469Z", - "iopub.status.busy": "2024-10-01T10:21:35.269141Z", - "iopub.status.idle": "2024-10-01T10:21:35.272740Z", - "shell.execute_reply": "2024-10-01T10:21:35.272218Z" + "iopub.execute_input": "2024-10-03T09:53:34.457267Z", + "iopub.status.busy": "2024-10-03T09:53:34.456937Z", + "iopub.status.idle": "2024-10-03T09:53:34.460600Z", + "shell.execute_reply": "2024-10-03T09:53:34.460010Z" } }, "outputs": [], @@ -152,10 +152,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.274685Z", - "iopub.status.busy": "2024-10-01T10:21:35.274378Z", - "iopub.status.idle": "2024-10-01T10:21:35.278190Z", - "shell.execute_reply": "2024-10-01T10:21:35.277650Z" + "iopub.execute_input": "2024-10-03T09:53:34.462592Z", + "iopub.status.busy": "2024-10-03T09:53:34.462231Z", + "iopub.status.idle": "2024-10-03T09:53:34.466026Z", + "shell.execute_reply": "2024-10-03T09:53:34.465469Z" } }, "outputs": [], @@ -183,10 +183,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.280167Z", - "iopub.status.busy": "2024-10-01T10:21:35.279789Z", - "iopub.status.idle": "2024-10-01T10:21:35.283331Z", - "shell.execute_reply": "2024-10-01T10:21:35.282749Z" + "iopub.execute_input": "2024-10-03T09:53:34.467934Z", + "iopub.status.busy": "2024-10-03T09:53:34.467629Z", + "iopub.status.idle": "2024-10-03T09:53:34.471364Z", + "shell.execute_reply": "2024-10-03T09:53:34.470702Z" } }, "outputs": [ @@ -235,10 +235,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.285388Z", - "iopub.status.busy": "2024-10-01T10:21:35.284915Z", - "iopub.status.idle": "2024-10-01T10:21:35.289006Z", - "shell.execute_reply": "2024-10-01T10:21:35.288352Z" + "iopub.execute_input": "2024-10-03T09:53:34.473608Z", + "iopub.status.busy": "2024-10-03T09:53:34.473229Z", + "iopub.status.idle": "2024-10-03T09:53:34.477021Z", + "shell.execute_reply": "2024-10-03T09:53:34.476500Z" } }, "outputs": [], @@ -260,10 +260,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.291373Z", - "iopub.status.busy": "2024-10-01T10:21:35.290905Z", - "iopub.status.idle": "2024-10-01T10:21:35.294548Z", - "shell.execute_reply": "2024-10-01T10:21:35.293935Z" + "iopub.execute_input": "2024-10-03T09:53:34.479123Z", + "iopub.status.busy": "2024-10-03T09:53:34.478614Z", + "iopub.status.idle": "2024-10-03T09:53:34.482176Z", + "shell.execute_reply": "2024-10-03T09:53:34.481631Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.296718Z", - "iopub.status.busy": "2024-10-01T10:21:35.296269Z", - "iopub.status.idle": "2024-10-01T10:21:35.303317Z", - "shell.execute_reply": "2024-10-01T10:21:35.302694Z" + "iopub.execute_input": "2024-10-03T09:53:34.484156Z", + "iopub.status.busy": "2024-10-03T09:53:34.483957Z", + "iopub.status.idle": "2024-10-03T09:53:34.491130Z", + "shell.execute_reply": "2024-10-03T09:53:34.490468Z" } }, "outputs": [ @@ -365,10 +365,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.305286Z", - "iopub.status.busy": "2024-10-01T10:21:35.304918Z", - "iopub.status.idle": "2024-10-01T10:21:35.309073Z", - "shell.execute_reply": "2024-10-01T10:21:35.308429Z" + "iopub.execute_input": "2024-10-03T09:53:34.493358Z", + "iopub.status.busy": "2024-10-03T09:53:34.492916Z", + "iopub.status.idle": "2024-10-03T09:53:34.496885Z", + "shell.execute_reply": "2024-10-03T09:53:34.496257Z" } }, "outputs": [ @@ -416,10 +416,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.311099Z", - "iopub.status.busy": "2024-10-01T10:21:35.310796Z", - "iopub.status.idle": "2024-10-01T10:21:35.314045Z", - "shell.execute_reply": "2024-10-01T10:21:35.313503Z" + "iopub.execute_input": "2024-10-03T09:53:34.499006Z", + "iopub.status.busy": "2024-10-03T09:53:34.498554Z", + "iopub.status.idle": "2024-10-03T09:53:34.501829Z", + "shell.execute_reply": "2024-10-03T09:53:34.501307Z" } }, "outputs": [], @@ -441,10 +441,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.315947Z", - "iopub.status.busy": "2024-10-01T10:21:35.315652Z", - "iopub.status.idle": "2024-10-01T10:21:35.319618Z", - "shell.execute_reply": "2024-10-01T10:21:35.319070Z" + "iopub.execute_input": "2024-10-03T09:53:34.503858Z", + "iopub.status.busy": "2024-10-03T09:53:34.503386Z", + "iopub.status.idle": "2024-10-03T09:53:34.507222Z", + "shell.execute_reply": "2024-10-03T09:53:34.506560Z" } }, "outputs": [ @@ -510,10 +510,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.321543Z", - "iopub.status.busy": "2024-10-01T10:21:35.321243Z", - "iopub.status.idle": "2024-10-01T10:21:35.324708Z", - "shell.execute_reply": "2024-10-01T10:21:35.324168Z" + "iopub.execute_input": "2024-10-03T09:53:34.509289Z", + "iopub.status.busy": "2024-10-03T09:53:34.508939Z", + "iopub.status.idle": "2024-10-03T09:53:34.512324Z", + "shell.execute_reply": "2024-10-03T09:53:34.511663Z" } }, "outputs": [ @@ -548,10 +548,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.326698Z", - "iopub.status.busy": "2024-10-01T10:21:35.326314Z", - "iopub.status.idle": "2024-10-01T10:21:35.329908Z", - "shell.execute_reply": "2024-10-01T10:21:35.329270Z" + "iopub.execute_input": "2024-10-03T09:53:34.514363Z", + "iopub.status.busy": "2024-10-03T09:53:34.513933Z", + "iopub.status.idle": "2024-10-03T09:53:34.517513Z", + "shell.execute_reply": "2024-10-03T09:53:34.516848Z" } }, "outputs": [ @@ -584,10 +584,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.332050Z", - "iopub.status.busy": "2024-10-01T10:21:35.331672Z", - "iopub.status.idle": "2024-10-01T10:21:35.335058Z", - "shell.execute_reply": "2024-10-01T10:21:35.334529Z" + "iopub.execute_input": "2024-10-03T09:53:34.519448Z", + "iopub.status.busy": "2024-10-03T09:53:34.519087Z", + "iopub.status.idle": "2024-10-03T09:53:34.522821Z", + "shell.execute_reply": "2024-10-03T09:53:34.522159Z" } }, "outputs": [ @@ -622,10 +622,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.337013Z", - "iopub.status.busy": "2024-10-01T10:21:35.336653Z", - "iopub.status.idle": "2024-10-01T10:21:35.340723Z", - "shell.execute_reply": "2024-10-01T10:21:35.340090Z" + "iopub.execute_input": "2024-10-03T09:53:34.525117Z", + "iopub.status.busy": "2024-10-03T09:53:34.524550Z", + "iopub.status.idle": "2024-10-03T09:53:34.528556Z", + "shell.execute_reply": "2024-10-03T09:53:34.527980Z" } }, "outputs": [ @@ -669,10 +669,10 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.342956Z", - "iopub.status.busy": "2024-10-01T10:21:35.342525Z", - "iopub.status.idle": "2024-10-01T10:21:35.347821Z", - "shell.execute_reply": "2024-10-01T10:21:35.347186Z" + "iopub.execute_input": "2024-10-03T09:53:34.530529Z", + "iopub.status.busy": "2024-10-03T09:53:34.530173Z", + "iopub.status.idle": "2024-10-03T09:53:34.535552Z", + "shell.execute_reply": "2024-10-03T09:53:34.534879Z" } }, "outputs": [ @@ -733,10 +733,10 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.349882Z", - "iopub.status.busy": "2024-10-01T10:21:35.349526Z", - "iopub.status.idle": "2024-10-01T10:21:35.353111Z", - "shell.execute_reply": "2024-10-01T10:21:35.352535Z" + "iopub.execute_input": "2024-10-03T09:53:34.537557Z", + "iopub.status.busy": "2024-10-03T09:53:34.537357Z", + "iopub.status.idle": "2024-10-03T09:53:34.540842Z", + "shell.execute_reply": "2024-10-03T09:53:34.540275Z" } }, "outputs": [], @@ -761,10 +761,10 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.355237Z", - "iopub.status.busy": "2024-10-01T10:21:35.354773Z", - "iopub.status.idle": "2024-10-01T10:21:35.364975Z", - "shell.execute_reply": "2024-10-01T10:21:35.364385Z" + "iopub.execute_input": "2024-10-03T09:53:34.542785Z", + "iopub.status.busy": "2024-10-03T09:53:34.542582Z", + "iopub.status.idle": "2024-10-03T09:53:34.552887Z", + "shell.execute_reply": "2024-10-03T09:53:34.552339Z" } }, "outputs": [], @@ -857,10 +857,10 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.366951Z", - "iopub.status.busy": "2024-10-01T10:21:35.366563Z", - "iopub.status.idle": "2024-10-01T10:21:35.369997Z", - "shell.execute_reply": "2024-10-01T10:21:35.369425Z" + "iopub.execute_input": "2024-10-03T09:53:34.554719Z", + "iopub.status.busy": "2024-10-03T09:53:34.554520Z", + "iopub.status.idle": "2024-10-03T09:53:34.558319Z", + "shell.execute_reply": "2024-10-03T09:53:34.557763Z" } }, "outputs": [ @@ -897,10 +897,10 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.372058Z", - "iopub.status.busy": "2024-10-01T10:21:35.371676Z", - "iopub.status.idle": "2024-10-01T10:21:35.376989Z", - "shell.execute_reply": "2024-10-01T10:21:35.376400Z" + "iopub.execute_input": "2024-10-03T09:53:34.560117Z", + "iopub.status.busy": "2024-10-03T09:53:34.559940Z", + "iopub.status.idle": "2024-10-03T09:53:34.565394Z", + "shell.execute_reply": "2024-10-03T09:53:34.564851Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb index a09e3e83b..471a11f7f 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": { - "iopub.execute_input": "2024-10-01T10:21:37.821174Z", - "iopub.status.busy": "2024-10-01T10:21:37.820574Z", - "iopub.status.idle": "2024-10-01T10:21:38.618818Z", - "shell.execute_reply": "2024-10-01T10:21:38.617989Z" + "iopub.execute_input": "2024-10-03T09:53:37.029702Z", + "iopub.status.busy": "2024-10-03T09:53:37.029512Z", + "iopub.status.idle": "2024-10-03T09:53:37.826943Z", + "shell.execute_reply": "2024-10-03T09:53:37.826135Z" } }, "outputs": [], @@ -103,10 +103,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.621301Z", - "iopub.status.busy": "2024-10-01T10:21:38.621084Z", - "iopub.status.idle": "2024-10-01T10:21:38.651744Z", - "shell.execute_reply": "2024-10-01T10:21:38.651083Z" + "iopub.execute_input": "2024-10-03T09:53:37.829354Z", + "iopub.status.busy": "2024-10-03T09:53:37.829140Z", + "iopub.status.idle": "2024-10-03T09:53:37.859411Z", + "shell.execute_reply": "2024-10-03T09:53:37.858638Z" } }, "outputs": [], @@ -149,10 +149,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.654226Z", - "iopub.status.busy": "2024-10-01T10:21:38.653834Z", - "iopub.status.idle": "2024-10-01T10:21:38.931262Z", - "shell.execute_reply": "2024-10-01T10:21:38.930514Z" + "iopub.execute_input": "2024-10-03T09:53:37.861808Z", + "iopub.status.busy": "2024-10-03T09:53:37.861481Z", + "iopub.status.idle": "2024-10-03T09:53:38.135604Z", + "shell.execute_reply": "2024-10-03T09:53:38.134960Z" } }, "outputs": [ @@ -196,10 +196,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.933516Z", - "iopub.status.busy": "2024-10-01T10:21:38.933264Z", - "iopub.status.idle": "2024-10-01T10:21:39.065959Z", - "shell.execute_reply": "2024-10-01T10:21:39.065329Z" + "iopub.execute_input": "2024-10-03T09:53:38.137950Z", + "iopub.status.busy": "2024-10-03T09:53:38.137502Z", + "iopub.status.idle": "2024-10-03T09:53:38.269859Z", + "shell.execute_reply": "2024-10-03T09:53:38.269248Z" } }, "outputs": [ @@ -243,10 +243,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.068045Z", - "iopub.status.busy": "2024-10-01T10:21:39.067838Z", - "iopub.status.idle": "2024-10-01T10:21:39.076495Z", - "shell.execute_reply": "2024-10-01T10:21:39.075931Z" + "iopub.execute_input": "2024-10-03T09:53:38.272256Z", + "iopub.status.busy": "2024-10-03T09:53:38.271871Z", + "iopub.status.idle": "2024-10-03T09:53:38.280375Z", + "shell.execute_reply": "2024-10-03T09:53:38.279751Z" } }, "outputs": [ @@ -290,10 +290,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.078383Z", - "iopub.status.busy": "2024-10-01T10:21:39.078181Z", - "iopub.status.idle": "2024-10-01T10:21:39.095112Z", - "shell.execute_reply": "2024-10-01T10:21:39.094537Z" + "iopub.execute_input": "2024-10-03T09:53:38.282442Z", + "iopub.status.busy": "2024-10-03T09:53:38.281980Z", + "iopub.status.idle": "2024-10-03T09:53:38.299215Z", + "shell.execute_reply": "2024-10-03T09:53:38.298551Z" } }, "outputs": [ @@ -337,10 +337,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.097092Z", - "iopub.status.busy": "2024-10-01T10:21:39.096877Z", - "iopub.status.idle": "2024-10-01T10:21:39.215347Z", - "shell.execute_reply": "2024-10-01T10:21:39.214752Z" + "iopub.execute_input": "2024-10-03T09:53:38.301612Z", + "iopub.status.busy": "2024-10-03T09:53:38.301136Z", + "iopub.status.idle": "2024-10-03T09:53:38.419523Z", + "shell.execute_reply": "2024-10-03T09:53:38.418841Z" } }, "outputs": [ @@ -400,10 +400,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.217531Z", - "iopub.status.busy": "2024-10-01T10:21:39.217320Z", - "iopub.status.idle": "2024-10-01T10:21:39.313393Z", - "shell.execute_reply": "2024-10-01T10:21:39.312662Z" + "iopub.execute_input": "2024-10-03T09:53:38.421923Z", + "iopub.status.busy": "2024-10-03T09:53:38.421414Z", + "iopub.status.idle": "2024-10-03T09:53:38.515903Z", + "shell.execute_reply": "2024-10-03T09:53:38.515301Z" } }, "outputs": [ @@ -456,10 +456,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.315719Z", - "iopub.status.busy": "2024-10-01T10:21:39.315219Z", - "iopub.status.idle": "2024-10-01T10:21:39.388710Z", - "shell.execute_reply": "2024-10-01T10:21:39.387983Z" + "iopub.execute_input": "2024-10-03T09:53:38.518071Z", + "iopub.status.busy": "2024-10-03T09:53:38.517679Z", + "iopub.status.idle": "2024-10-03T09:53:38.591539Z", + "shell.execute_reply": "2024-10-03T09:53:38.590857Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb index bec37eafb..9841e393f 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": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:41.326725Z", - "iopub.status.busy": "2024-10-01T10:21:41.326155Z", - "iopub.status.idle": "2024-10-01T10:21:42.137111Z", - "shell.execute_reply": "2024-10-01T10:21:42.136334Z" + "iopub.execute_input": "2024-10-03T09:53:40.365376Z", + "iopub.status.busy": "2024-10-03T09:53:40.364829Z", + "iopub.status.idle": "2024-10-03T09:53:41.156781Z", + "shell.execute_reply": "2024-10-03T09:53:41.155887Z" } }, "outputs": [], @@ -79,10 +79,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.139932Z", - "iopub.status.busy": "2024-10-01T10:21:42.139501Z", - "iopub.status.idle": "2024-10-01T10:21:42.170809Z", - "shell.execute_reply": "2024-10-01T10:21:42.170151Z" + "iopub.execute_input": "2024-10-03T09:53:41.159607Z", + "iopub.status.busy": "2024-10-03T09:53:41.159193Z", + "iopub.status.idle": "2024-10-03T09:53:41.190016Z", + "shell.execute_reply": "2024-10-03T09:53:41.189404Z" } }, "outputs": [], @@ -123,10 +123,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.173320Z", - "iopub.status.busy": "2024-10-01T10:21:42.172853Z", - "iopub.status.idle": "2024-10-01T10:21:42.610616Z", - "shell.execute_reply": "2024-10-01T10:21:42.609890Z" + "iopub.execute_input": "2024-10-03T09:53:41.192396Z", + "iopub.status.busy": "2024-10-03T09:53:41.191997Z", + "iopub.status.idle": "2024-10-03T09:53:41.609066Z", + "shell.execute_reply": "2024-10-03T09:53:41.608387Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.612789Z", - "iopub.status.busy": "2024-10-01T10:21:42.612376Z", - "iopub.status.idle": "2024-10-01T10:21:42.726609Z", - "shell.execute_reply": "2024-10-01T10:21:42.725883Z" + "iopub.execute_input": "2024-10-03T09:53:41.611297Z", + "iopub.status.busy": "2024-10-03T09:53:41.610852Z", + "iopub.status.idle": "2024-10-03T09:53:41.722451Z", + "shell.execute_reply": "2024-10-03T09:53:41.721774Z" } }, "outputs": [ @@ -207,10 +207,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.728917Z", - "iopub.status.busy": "2024-10-01T10:21:42.728504Z", - "iopub.status.idle": "2024-10-01T10:21:42.929400Z", - "shell.execute_reply": "2024-10-01T10:21:42.928749Z" + "iopub.execute_input": "2024-10-03T09:53:41.724817Z", + "iopub.status.busy": "2024-10-03T09:53:41.724390Z", + "iopub.status.idle": "2024-10-03T09:53:41.924048Z", + "shell.execute_reply": "2024-10-03T09:53:41.923429Z" } }, "outputs": [ @@ -255,10 +255,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.931679Z", - "iopub.status.busy": "2024-10-01T10:21:42.931276Z", - "iopub.status.idle": "2024-10-01T10:21:43.092553Z", - "shell.execute_reply": "2024-10-01T10:21:43.091899Z" + "iopub.execute_input": "2024-10-03T09:53:41.926283Z", + "iopub.status.busy": "2024-10-03T09:53:41.925871Z", + "iopub.status.idle": "2024-10-03T09:53:42.084576Z", + "shell.execute_reply": "2024-10-03T09:53:42.083899Z" } }, "outputs": [ @@ -303,10 +303,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:43.094821Z", - "iopub.status.busy": "2024-10-01T10:21:43.094408Z", - "iopub.status.idle": "2024-10-01T10:21:44.860368Z", - "shell.execute_reply": "2024-10-01T10:21:44.859636Z" + "iopub.execute_input": "2024-10-03T09:53:42.086953Z", + "iopub.status.busy": "2024-10-03T09:53:42.086545Z", + "iopub.status.idle": "2024-10-03T09:53:43.836453Z", + "shell.execute_reply": "2024-10-03T09:53:43.835742Z" } }, "outputs": [ @@ -351,10 +351,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:44.862696Z", - "iopub.status.busy": "2024-10-01T10:21:44.862182Z", - "iopub.status.idle": "2024-10-01T10:21:47.151307Z", - "shell.execute_reply": "2024-10-01T10:21:47.150583Z" + "iopub.execute_input": "2024-10-03T09:53:43.838762Z", + "iopub.status.busy": "2024-10-03T09:53:43.838541Z", + "iopub.status.idle": "2024-10-03T09:53:46.087265Z", + "shell.execute_reply": "2024-10-03T09:53:46.086510Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb index 84066bb72..b1a09c50c 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": "2024-10-01T10:21:48.814953Z", - "iopub.status.busy": "2024-10-01T10:21:48.814455Z", - "iopub.status.idle": "2024-10-01T10:21:49.625080Z", - "shell.execute_reply": "2024-10-01T10:21:49.624212Z" + "iopub.execute_input": "2024-10-03T09:53:47.686836Z", + "iopub.status.busy": "2024-10-03T09:53:47.686621Z", + "iopub.status.idle": "2024-10-03T09:53:48.485520Z", + "shell.execute_reply": "2024-10-03T09:53:48.484603Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:49.627765Z", - "iopub.status.busy": "2024-10-01T10:21:49.627356Z", - "iopub.status.idle": "2024-10-01T10:21:49.658492Z", - "shell.execute_reply": "2024-10-01T10:21:49.657831Z" + "iopub.execute_input": "2024-10-03T09:53:48.488070Z", + "iopub.status.busy": "2024-10-03T09:53:48.487866Z", + "iopub.status.idle": "2024-10-03T09:53:48.518976Z", + "shell.execute_reply": "2024-10-03T09:53:48.518304Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:49.660789Z", - "iopub.status.busy": "2024-10-01T10:21:49.660517Z", - "iopub.status.idle": "2024-10-01T10:21:50.155126Z", - "shell.execute_reply": "2024-10-01T10:21:50.154469Z" + "iopub.execute_input": "2024-10-03T09:53:48.521438Z", + "iopub.status.busy": "2024-10-03T09:53:48.521097Z", + "iopub.status.idle": "2024-10-03T09:53:49.023871Z", + "shell.execute_reply": "2024-10-03T09:53:49.023158Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:50.157391Z", - "iopub.status.busy": "2024-10-01T10:21:50.156939Z", - "iopub.status.idle": "2024-10-01T10:21:50.455120Z", - "shell.execute_reply": "2024-10-01T10:21:50.454384Z" + "iopub.execute_input": "2024-10-03T09:53:49.026236Z", + "iopub.status.busy": "2024-10-03T09:53:49.025963Z", + "iopub.status.idle": "2024-10-03T09:53:49.320740Z", + "shell.execute_reply": "2024-10-03T09:53:49.320021Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb index 2f06803cc..5ab01e354 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": "2024-10-01T10:21:51.946600Z", - "iopub.status.busy": "2024-10-01T10:21:51.946193Z", - "iopub.status.idle": "2024-10-01T10:21:52.775471Z", - "shell.execute_reply": "2024-10-01T10:21:52.774694Z" + "iopub.execute_input": "2024-10-03T09:53:50.821936Z", + "iopub.status.busy": "2024-10-03T09:53:50.821463Z", + "iopub.status.idle": "2024-10-03T09:53:51.626330Z", + "shell.execute_reply": "2024-10-03T09:53:51.625563Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:52.778275Z", - "iopub.status.busy": "2024-10-01T10:21:52.777839Z", - "iopub.status.idle": "2024-10-01T10:21:52.809576Z", - "shell.execute_reply": "2024-10-01T10:21:52.808846Z" + "iopub.execute_input": "2024-10-03T09:53:51.629015Z", + "iopub.status.busy": "2024-10-03T09:53:51.628599Z", + "iopub.status.idle": "2024-10-03T09:53:51.659114Z", + "shell.execute_reply": "2024-10-03T09:53:51.658483Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:52.812049Z", - "iopub.status.busy": "2024-10-01T10:21:52.811709Z", - "iopub.status.idle": "2024-10-01T10:21:53.314250Z", - "shell.execute_reply": "2024-10-01T10:21:53.313504Z" + "iopub.execute_input": "2024-10-03T09:53:51.661347Z", + "iopub.status.busy": "2024-10-03T09:53:51.661019Z", + "iopub.status.idle": "2024-10-03T09:53:52.160649Z", + "shell.execute_reply": "2024-10-03T09:53:52.159884Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:53.316448Z", - "iopub.status.busy": "2024-10-01T10:21:53.316177Z", - "iopub.status.idle": "2024-10-01T10:21:53.614222Z", - "shell.execute_reply": "2024-10-01T10:21:53.613471Z" + "iopub.execute_input": "2024-10-03T09:53:52.163142Z", + "iopub.status.busy": "2024-10-03T09:53:52.162671Z", + "iopub.status.idle": "2024-10-03T09:53:52.461865Z", + "shell.execute_reply": "2024-10-03T09:53:52.461190Z" } }, "outputs": [ diff --git a/.doctrees/nmodl.doctree b/.doctrees/nmodl.doctree index 610b9a47e522213398b31d26fe1385987e50e8b9..d32b9c11579f023a917e90a7d707293b399198aa 100644 GIT binary patch delta 7315 zcmcgxeOQ#&v1g7T2&}LyyRg810Db@p0TENR(WoJ!_yI9~7vri+mRAH6NsWe}N$o9) 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Source code for nmodl.ode

     return f"{sp.ccode(x)} = {sp.ccode(solution, user_functions=custom_fcts)}"
-
[docs]def differentiate2c(expression, dependent_var, vars, prev_expressions=None): +
[docs]def differentiate2c( + expression, + dependent_var, + vars, + prev_expressions=None, + stepsize=1e-3, +): """Analytically differentiate supplied expression, return solution as C code. Expression should be of the form "f(x)", where "x" is @@ -706,11 +712,15 @@

Source code for nmodl.ode

         vars: set of all other variables used in expression, e.g. {"a", "b", "c"}
         prev_expressions: time-ordered list of preceeding expressions
                           to evaluate & substitute, e.g. ["b = x + c", "a = 12*b"]
+        stepsize: in case an analytic expression is not possible, finite differences are used;
+                  this argument sets the step size
 
     Returns:
         string containing analytic derivative of expression (including any substitutions
         of variables from supplied prev_expressions) w.r.t. dependent_var as C code.
     """
+    if stepsize <= 0:
+        raise ValueError("arg `stepsize` must be > 0")
     prev_expressions = prev_expressions or []
     # every symbol (a.k.a variable) that SymPy
     # is going to manipulate needs to be declared
@@ -754,15 +764,27 @@ 
Source code for nmodl.ode
     # differentiate w.r.t. x
     diff = expr.diff(x).simplify()
 
+    # could be something generic like f'(x), in which case we use finite differences
+    if needs_finite_differences(diff):
+        diff = (
+            transform_expression(diff, discretize_derivative)
+            .subs({finite_difference_step_variable(x): stepsize})
+            .evalf()
+        )
+
+    # the codegen method does not like undefined function calls, so we extract
+    # them here
+    custom_fcts = {str(f.func): str(f.func) for f in diff.atoms(sp.Function)}
+
     # try to simplify expression in terms of existing variables
     # ignore any exceptions here, since we already have a valid solution
     # so if this further simplification step fails the error is not fatal
     try:
         # if expression is equal to one of the supplied vars, replace with this var
         # can do a simple string comparison here since a var cannot be further simplified
-        diff_as_string = sp.ccode(diff)
+        diff_as_string = sp.ccode(diff, user_functions=custom_fcts)
         for v in sympy_vars:
-            if diff_as_string == sp.ccode(sympy_vars[v]):
+            if diff_as_string == sp.ccode(sympy_vars[v], user_functions=custom_fcts):
                 diff = sympy_vars[v]
 
         # or if equal to rhs of one of the supplied equations, replace with lhs
@@ -783,7 +805,7 @@ 
Source code for nmodl.ode
         pass
 
     # return result as C code in NEURON format
-    return sp.ccode(diff.evalf())

+    return sp.ccode(diff.evalf(), user_functions=custom_fcts)
diff --git a/doxygen/src_2main_8cpp_source.html b/doxygen/src_2main_8cpp_source.html index 70876cab3..949fa72a6 100644 --- a/doxygen/src_2main_8cpp_source.html +++ b/doxygen/src_2main_8cpp_source.html @@ -410,104 +410,104 @@
314  /// create file path for nmodl file
315  auto filepath = [scratch_dir, modfile](const std::string& suffix) {
316  static int count = 0;
-
317  return fmt::format(
-
318  "{}/{}.{}.{}.mod", scratch_dir, modfile, std::to_string(count++), suffix);
-
319  };
-
320 
-
321  /// driver object creates lexer and parser, just call parser method
-
322  NmodlDriver driver;
-
323 
-
324  /// parse mod file and construct ast
-
325  const auto& ast = driver.parse_file(file);
-
326 
-
327  /// whether to update existing symbol table or create new
-
328  /// one whenever we run symtab visitor.
-
329  bool update_symtab = false;
-
330 
-
331  /// just visit the ast
-
332  AstVisitor().visit_program(*ast);
-
333 
-
334  {
-
335  logger->info("Running argument renaming visitor");
-
336  RenameFunctionArgumentsVisitor().visit_program(*ast);
-
337  }
-
338 
-
339  /// construct symbol table
-
340  {
-
341  logger->info("Running symtab visitor");
-
342  SymtabVisitor(update_symtab).visit_program(*ast);
-
343  }
-
344 
-
345  /// Check some rules that ast should follow
-
346  {
-
347  logger->info("Running semantic analysis visitor");
-
348  if (SemanticAnalysisVisitor(oacc_backend).check(*ast)) {
-
349  return 1;
-
350  }
-
351  }
-
352 
-
353  /// use cnexp instead of after_cvode solve method
-
354  {
-
355  logger->info("Running CVode to cnexp visitor");
-
356  AfterCVodeToCnexpVisitor().visit_program(*ast);
-
357  ast_to_nmodl(*ast, filepath("after_cvode_to_cnexp"));
-
358  }
-
359 
-
360  /// GLOBAL to RANGE rename visitor
-
361  if (nmodl_global_to_range) {
-
362  // make sure to run perf visitor because code generator
-
363  // looks for read/write counts const/non-const declaration
-
364  PerfVisitor().visit_program(*ast);
-
365  // make sure to run the GlobalToRange visitor after all the
-
366  // reinitializations of Symtab
-
367  logger->info("Running GlobalToRange visitor");
-
368  GlobalToRangeVisitor(*ast).visit_program(*ast);
-
369  SymtabVisitor(update_symtab).visit_program(*ast);
-
370  ast_to_nmodl(*ast, filepath("global_to_range"));
-
371  }
-
372 
-
373  /// LOCAL to ASSIGNED visitor
-
374  if (nmodl_local_to_range) {
-
375  logger->info("Running LOCAL to ASSIGNED visitor");
-
376  PerfVisitor().visit_program(*ast);
-
377  LocalToAssignedVisitor().visit_program(*ast);
-
378  SymtabVisitor(update_symtab).visit_program(*ast);
-
379  ast_to_nmodl(*ast, filepath("local_to_assigned"));
-
380  }
-
381 
-
382  {
-
383  // Compatibility Checking
-
384  logger->info("Running code compatibility checker");
-
385  // run perfvisitor to update read/write counts
-
386  PerfVisitor().visit_program(*ast);
-
387 
-
388  auto compatibility_visitor = CodegenCompatibilityVisitor(simulator_name);
-
389  // If we want to just check compatibility we return the result
-
390  if (only_check_compatibility) {
-
391  return compatibility_visitor.find_unhandled_ast_nodes(*ast);
-
392  }
-
393 
-
394  // If there is an incompatible construct and code generation is not forced exit NMODL
-
395  if (compatibility_visitor.find_unhandled_ast_nodes(*ast) && !force_codegen) {
-
396  return 1;
-
397  }
-
398  }
-
399 
-
400  if (show_symtab) {
-
401  logger->info("Printing symbol table");
-
402  auto symtab = ast->get_model_symbol_table();
-
403  symtab->print(std::cout);
-
404  }
-
405 
-
406  ast_to_nmodl(*ast, filepath("ast"));
+
317 
+
318  auto filename = fmt::format("{}.{}.{}.mod", modfile, std::to_string(count++), suffix);
+
319 
+
320  return (std::filesystem::path(scratch_dir) / filename).string();
+
321  };
+
322 
+
323  /// driver object creates lexer and parser, just call parser method
+
324  NmodlDriver driver;
+
325 
+
326  /// parse mod file and construct ast
+
327  const auto& ast = driver.parse_file(file);
+
328 
+
329  /// whether to update existing symbol table or create new
+
330  /// one whenever we run symtab visitor.
+
331  bool update_symtab = false;
+
332 
+
333  /// just visit the ast
+
334  AstVisitor().visit_program(*ast);
+
335 
+
336  {
+
337  logger->info("Running argument renaming visitor");
+
338  RenameFunctionArgumentsVisitor().visit_program(*ast);
+
339  }
+
340 
+
341  /// construct symbol table
+
342  {
+
343  logger->info("Running symtab visitor");
+
344  SymtabVisitor(update_symtab).visit_program(*ast);
+
345  }
+
346 
+
347  /// Check some rules that ast should follow
+
348  {
+
349  logger->info("Running semantic analysis visitor");
+
350  if (SemanticAnalysisVisitor(oacc_backend).check(*ast)) {
+
351  return 1;
+
352  }
+
353  }
+
354 
+
355  /// use cnexp instead of after_cvode solve method
+
356  {
+
357  logger->info("Running CVode to cnexp visitor");
+
358  AfterCVodeToCnexpVisitor().visit_program(*ast);
+
359  ast_to_nmodl(*ast, filepath("after_cvode_to_cnexp"));
+
360  }
+
361 
+
362  /// GLOBAL to RANGE rename visitor
+
363  if (nmodl_global_to_range) {
+
364  // make sure to run perf visitor because code generator
+
365  // looks for read/write counts const/non-const declaration
+
366  PerfVisitor().visit_program(*ast);
+
367  // make sure to run the GlobalToRange visitor after all the
+
368  // reinitializations of Symtab
+
369  logger->info("Running GlobalToRange visitor");
+
370  GlobalToRangeVisitor(*ast).visit_program(*ast);
+
371  SymtabVisitor(update_symtab).visit_program(*ast);
+
372  ast_to_nmodl(*ast, filepath("global_to_range"));
+
373  }
+
374 
+
375  /// LOCAL to ASSIGNED visitor
+
376  if (nmodl_local_to_range) {
+
377  logger->info("Running LOCAL to ASSIGNED visitor");
+
378  PerfVisitor().visit_program(*ast);
+
379  LocalToAssignedVisitor().visit_program(*ast);
+
380  SymtabVisitor(update_symtab).visit_program(*ast);
+
381  ast_to_nmodl(*ast, filepath("local_to_assigned"));
+
382  }
+
383 
+
384  {
+
385  // Compatibility Checking
+
386  logger->info("Running code compatibility checker");
+
387  // run perfvisitor to update read/write counts
+
388  PerfVisitor().visit_program(*ast);
+
389 
+
390  auto compatibility_visitor = CodegenCompatibilityVisitor(simulator_name);
+
391  // If we want to just check compatibility we return the result
+
392  if (only_check_compatibility) {
+
393  return compatibility_visitor.find_unhandled_ast_nodes(*ast);
+
394  }
+
395 
+
396  // If there is an incompatible construct and code generation is not forced exit NMODL
+
397  if (compatibility_visitor.find_unhandled_ast_nodes(*ast) && !force_codegen) {
+
398  return 1;
+
399  }
+
400  }
+
401 
+
402  if (show_symtab) {
+
403  logger->info("Printing symbol table");
+
404  auto symtab = ast->get_model_symbol_table();
+
405  symtab->print(std::cout);
+
406  }
407 
-
408  if (json_ast) {
-
409  std::string file{scratch_dir};
-
410  file += "/";
-
411  file += modfile;
-
412  file += ".ast.json";
-
413  logger->info("Writing AST into {}", file);
-
414  JSONVisitor(file).write(*ast);
+
408  ast_to_nmodl(*ast, filepath("ast"));
+
409 
+
410  if (json_ast) {
+
411  std::filesystem::path file{scratch_dir};
+
412  file /= modfile + ".ast.json";
+
413  logger->info("Writing AST into {}", file.string());
+
414  JSONVisitor(file.string()).write(*ast);
415  }
416 
417  if (verbatim_rename) {
diff --git a/nmodl.html b/nmodl.html index 8935200ef..63021f19b 100644 --- a/nmodl.html +++ b/nmodl.html @@ -340,7 +340,7 @@

Submodules

nmodl.ode module

-nmodl.ode.differentiate2c(expression, dependent_var, vars, prev_expressions=None)[source]
+nmodl.ode.differentiate2c(expression, dependent_var, vars, prev_expressions=None, stepsize=0.001)[source]

Analytically differentiate supplied expression, return solution as C code.

Expression should be of the form “f(x)”, where “x” is the dependent variable, and the function returns df(x)/dx

@@ -364,6 +364,8 @@

SubmodulesReturns: diff --git a/notebooks/nmodl-kinetic-schemes.ipynb b/notebooks/nmodl-kinetic-schemes.ipynb index f77d90137..e314791b0 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": "2024-10-01T10:21:28.231435Z", - "iopub.status.busy": "2024-10-01T10:21:28.231238Z", - "iopub.status.idle": "2024-10-01T10:21:29.033845Z", - "shell.execute_reply": "2024-10-01T10:21:29.033024Z" + "iopub.execute_input": "2024-10-03T09:53:27.189915Z", + "iopub.status.busy": "2024-10-03T09:53:27.189431Z", + "iopub.status.idle": "2024-10-03T09:53:27.978488Z", + "shell.execute_reply": "2024-10-03T09:53:27.977663Z" } }, "outputs": [], @@ -169,10 +169,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.036443Z", - "iopub.status.busy": "2024-10-01T10:21:29.036030Z", - "iopub.status.idle": "2024-10-01T10:21:29.066797Z", - "shell.execute_reply": "2024-10-01T10:21:29.066164Z" + "iopub.execute_input": "2024-10-03T09:53:27.981149Z", + "iopub.status.busy": "2024-10-03T09:53:27.980922Z", + "iopub.status.idle": "2024-10-03T09:53:28.011658Z", + "shell.execute_reply": "2024-10-03T09:53:28.011033Z" } }, "outputs": [], @@ -277,10 +277,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.069059Z", - "iopub.status.busy": "2024-10-01T10:21:29.068722Z", - "iopub.status.idle": "2024-10-01T10:21:29.073735Z", - "shell.execute_reply": "2024-10-01T10:21:29.073036Z" + "iopub.execute_input": "2024-10-03T09:53:28.014217Z", + "iopub.status.busy": "2024-10-03T09:53:28.013738Z", + "iopub.status.idle": "2024-10-03T09:53:28.018271Z", + "shell.execute_reply": "2024-10-03T09:53:28.017636Z" } }, "outputs": [ @@ -323,10 +323,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.103779Z", - "iopub.status.busy": "2024-10-01T10:21:29.103327Z", - "iopub.status.idle": "2024-10-01T10:21:29.107488Z", - "shell.execute_reply": "2024-10-01T10:21:29.106918Z" + "iopub.execute_input": "2024-10-03T09:53:28.048586Z", + "iopub.status.busy": "2024-10-03T09:53:28.048123Z", + "iopub.status.idle": "2024-10-03T09:53:28.051868Z", + "shell.execute_reply": "2024-10-03T09:53:28.051320Z" } }, "outputs": [ @@ -367,10 +367,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.109512Z", - "iopub.status.busy": "2024-10-01T10:21:29.109150Z", - "iopub.status.idle": "2024-10-01T10:21:29.112981Z", - "shell.execute_reply": "2024-10-01T10:21:29.112414Z" + "iopub.execute_input": "2024-10-03T09:53:28.054128Z", + "iopub.status.busy": "2024-10-03T09:53:28.053610Z", + "iopub.status.idle": "2024-10-03T09:53:28.057453Z", + "shell.execute_reply": "2024-10-03T09:53:28.056897Z" }, "scrolled": true }, @@ -412,10 +412,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.114916Z", - "iopub.status.busy": "2024-10-01T10:21:29.114547Z", - "iopub.status.idle": "2024-10-01T10:21:29.118506Z", - "shell.execute_reply": "2024-10-01T10:21:29.117935Z" + "iopub.execute_input": "2024-10-03T09:53:28.059453Z", + "iopub.status.busy": "2024-10-03T09:53:28.059082Z", + "iopub.status.idle": "2024-10-03T09:53:28.062912Z", + "shell.execute_reply": "2024-10-03T09:53:28.062353Z" }, "scrolled": true }, @@ -459,10 +459,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:29.120491Z", - "iopub.status.busy": "2024-10-01T10:21:29.120121Z", - "iopub.status.idle": "2024-10-01T10:21:29.124711Z", - "shell.execute_reply": "2024-10-01T10:21:29.124162Z" + "iopub.execute_input": "2024-10-03T09:53:28.064721Z", + "iopub.status.busy": "2024-10-03T09:53:28.064520Z", + "iopub.status.idle": "2024-10-03T09:53:28.069195Z", + "shell.execute_reply": "2024-10-03T09:53:28.068634Z" } }, "outputs": [ diff --git a/notebooks/nmodl-python-tutorial.ipynb b/notebooks/nmodl-python-tutorial.ipynb index 8bf04d8fc..adf221707 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": "2024-10-01T10:21:34.429599Z", - "iopub.status.busy": "2024-10-01T10:21:34.429205Z", - "iopub.status.idle": "2024-10-01T10:21:35.235253Z", - "shell.execute_reply": "2024-10-01T10:21:35.234452Z" + "iopub.execute_input": "2024-10-03T09:53:33.628062Z", + "iopub.status.busy": "2024-10-03T09:53:33.627869Z", + "iopub.status.idle": "2024-10-03T09:53:34.423988Z", + "shell.execute_reply": "2024-10-03T09:53:34.423097Z" } }, "outputs": [], @@ -63,10 +63,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.237787Z", - "iopub.status.busy": "2024-10-01T10:21:35.237566Z", - "iopub.status.idle": "2024-10-01T10:21:35.267042Z", - "shell.execute_reply": "2024-10-01T10:21:35.266427Z" + "iopub.execute_input": "2024-10-03T09:53:34.426837Z", + "iopub.status.busy": "2024-10-03T09:53:34.426419Z", + "iopub.status.idle": "2024-10-03T09:53:34.455042Z", + "shell.execute_reply": "2024-10-03T09:53:34.454411Z" } }, "outputs": [], @@ -86,10 +86,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.269469Z", - "iopub.status.busy": "2024-10-01T10:21:35.269141Z", - "iopub.status.idle": "2024-10-01T10:21:35.272740Z", - "shell.execute_reply": "2024-10-01T10:21:35.272218Z" + "iopub.execute_input": "2024-10-03T09:53:34.457267Z", + "iopub.status.busy": "2024-10-03T09:53:34.456937Z", + "iopub.status.idle": "2024-10-03T09:53:34.460600Z", + "shell.execute_reply": "2024-10-03T09:53:34.460010Z" } }, "outputs": [], @@ -152,10 +152,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.274685Z", - "iopub.status.busy": "2024-10-01T10:21:35.274378Z", - "iopub.status.idle": "2024-10-01T10:21:35.278190Z", - "shell.execute_reply": "2024-10-01T10:21:35.277650Z" + "iopub.execute_input": "2024-10-03T09:53:34.462592Z", + "iopub.status.busy": "2024-10-03T09:53:34.462231Z", + "iopub.status.idle": "2024-10-03T09:53:34.466026Z", + "shell.execute_reply": "2024-10-03T09:53:34.465469Z" } }, "outputs": [], @@ -183,10 +183,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.280167Z", - "iopub.status.busy": "2024-10-01T10:21:35.279789Z", - "iopub.status.idle": "2024-10-01T10:21:35.283331Z", - "shell.execute_reply": "2024-10-01T10:21:35.282749Z" + "iopub.execute_input": "2024-10-03T09:53:34.467934Z", + "iopub.status.busy": "2024-10-03T09:53:34.467629Z", + "iopub.status.idle": "2024-10-03T09:53:34.471364Z", + "shell.execute_reply": "2024-10-03T09:53:34.470702Z" } }, "outputs": [ @@ -235,10 +235,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.285388Z", - "iopub.status.busy": "2024-10-01T10:21:35.284915Z", - "iopub.status.idle": "2024-10-01T10:21:35.289006Z", - "shell.execute_reply": "2024-10-01T10:21:35.288352Z" + "iopub.execute_input": "2024-10-03T09:53:34.473608Z", + "iopub.status.busy": "2024-10-03T09:53:34.473229Z", + "iopub.status.idle": "2024-10-03T09:53:34.477021Z", + "shell.execute_reply": "2024-10-03T09:53:34.476500Z" } }, "outputs": [], @@ -260,10 +260,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.291373Z", - "iopub.status.busy": "2024-10-01T10:21:35.290905Z", - "iopub.status.idle": "2024-10-01T10:21:35.294548Z", - "shell.execute_reply": "2024-10-01T10:21:35.293935Z" + "iopub.execute_input": "2024-10-03T09:53:34.479123Z", + "iopub.status.busy": "2024-10-03T09:53:34.478614Z", + "iopub.status.idle": "2024-10-03T09:53:34.482176Z", + "shell.execute_reply": "2024-10-03T09:53:34.481631Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.296718Z", - "iopub.status.busy": "2024-10-01T10:21:35.296269Z", - "iopub.status.idle": "2024-10-01T10:21:35.303317Z", - "shell.execute_reply": "2024-10-01T10:21:35.302694Z" + "iopub.execute_input": "2024-10-03T09:53:34.484156Z", + "iopub.status.busy": "2024-10-03T09:53:34.483957Z", + "iopub.status.idle": "2024-10-03T09:53:34.491130Z", + "shell.execute_reply": "2024-10-03T09:53:34.490468Z" } }, "outputs": [ @@ -365,10 +365,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.305286Z", - "iopub.status.busy": "2024-10-01T10:21:35.304918Z", - "iopub.status.idle": "2024-10-01T10:21:35.309073Z", - "shell.execute_reply": "2024-10-01T10:21:35.308429Z" + "iopub.execute_input": "2024-10-03T09:53:34.493358Z", + "iopub.status.busy": "2024-10-03T09:53:34.492916Z", + "iopub.status.idle": "2024-10-03T09:53:34.496885Z", + "shell.execute_reply": "2024-10-03T09:53:34.496257Z" } }, "outputs": [ @@ -416,10 +416,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.311099Z", - "iopub.status.busy": "2024-10-01T10:21:35.310796Z", - "iopub.status.idle": "2024-10-01T10:21:35.314045Z", - "shell.execute_reply": "2024-10-01T10:21:35.313503Z" + "iopub.execute_input": "2024-10-03T09:53:34.499006Z", + "iopub.status.busy": "2024-10-03T09:53:34.498554Z", + "iopub.status.idle": "2024-10-03T09:53:34.501829Z", + "shell.execute_reply": "2024-10-03T09:53:34.501307Z" } }, "outputs": [], @@ -441,10 +441,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.315947Z", - "iopub.status.busy": "2024-10-01T10:21:35.315652Z", - "iopub.status.idle": "2024-10-01T10:21:35.319618Z", - "shell.execute_reply": "2024-10-01T10:21:35.319070Z" + "iopub.execute_input": "2024-10-03T09:53:34.503858Z", + "iopub.status.busy": "2024-10-03T09:53:34.503386Z", + "iopub.status.idle": "2024-10-03T09:53:34.507222Z", + "shell.execute_reply": "2024-10-03T09:53:34.506560Z" } }, "outputs": [ @@ -510,10 +510,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.321543Z", - "iopub.status.busy": "2024-10-01T10:21:35.321243Z", - "iopub.status.idle": "2024-10-01T10:21:35.324708Z", - "shell.execute_reply": "2024-10-01T10:21:35.324168Z" + "iopub.execute_input": "2024-10-03T09:53:34.509289Z", + "iopub.status.busy": "2024-10-03T09:53:34.508939Z", + "iopub.status.idle": "2024-10-03T09:53:34.512324Z", + "shell.execute_reply": "2024-10-03T09:53:34.511663Z" } }, "outputs": [ @@ -548,10 +548,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.326698Z", - "iopub.status.busy": "2024-10-01T10:21:35.326314Z", - "iopub.status.idle": "2024-10-01T10:21:35.329908Z", - "shell.execute_reply": "2024-10-01T10:21:35.329270Z" + "iopub.execute_input": "2024-10-03T09:53:34.514363Z", + "iopub.status.busy": "2024-10-03T09:53:34.513933Z", + "iopub.status.idle": "2024-10-03T09:53:34.517513Z", + "shell.execute_reply": "2024-10-03T09:53:34.516848Z" } }, "outputs": [ @@ -584,10 +584,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.332050Z", - "iopub.status.busy": "2024-10-01T10:21:35.331672Z", - "iopub.status.idle": "2024-10-01T10:21:35.335058Z", - "shell.execute_reply": "2024-10-01T10:21:35.334529Z" + "iopub.execute_input": "2024-10-03T09:53:34.519448Z", + "iopub.status.busy": "2024-10-03T09:53:34.519087Z", + "iopub.status.idle": "2024-10-03T09:53:34.522821Z", + "shell.execute_reply": "2024-10-03T09:53:34.522159Z" } }, "outputs": [ @@ -622,10 +622,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.337013Z", - "iopub.status.busy": "2024-10-01T10:21:35.336653Z", - "iopub.status.idle": "2024-10-01T10:21:35.340723Z", - "shell.execute_reply": "2024-10-01T10:21:35.340090Z" + "iopub.execute_input": "2024-10-03T09:53:34.525117Z", + "iopub.status.busy": "2024-10-03T09:53:34.524550Z", + "iopub.status.idle": "2024-10-03T09:53:34.528556Z", + "shell.execute_reply": "2024-10-03T09:53:34.527980Z" } }, "outputs": [ @@ -669,10 +669,10 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.342956Z", - "iopub.status.busy": "2024-10-01T10:21:35.342525Z", - "iopub.status.idle": "2024-10-01T10:21:35.347821Z", - "shell.execute_reply": "2024-10-01T10:21:35.347186Z" + "iopub.execute_input": "2024-10-03T09:53:34.530529Z", + "iopub.status.busy": "2024-10-03T09:53:34.530173Z", + "iopub.status.idle": "2024-10-03T09:53:34.535552Z", + "shell.execute_reply": "2024-10-03T09:53:34.534879Z" } }, "outputs": [ @@ -733,10 +733,10 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.349882Z", - "iopub.status.busy": "2024-10-01T10:21:35.349526Z", - "iopub.status.idle": "2024-10-01T10:21:35.353111Z", - "shell.execute_reply": "2024-10-01T10:21:35.352535Z" + "iopub.execute_input": "2024-10-03T09:53:34.537557Z", + "iopub.status.busy": "2024-10-03T09:53:34.537357Z", + "iopub.status.idle": "2024-10-03T09:53:34.540842Z", + "shell.execute_reply": "2024-10-03T09:53:34.540275Z" } }, "outputs": [], @@ -761,10 +761,10 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.355237Z", - "iopub.status.busy": "2024-10-01T10:21:35.354773Z", - "iopub.status.idle": "2024-10-01T10:21:35.364975Z", - "shell.execute_reply": "2024-10-01T10:21:35.364385Z" + "iopub.execute_input": "2024-10-03T09:53:34.542785Z", + "iopub.status.busy": "2024-10-03T09:53:34.542582Z", + "iopub.status.idle": "2024-10-03T09:53:34.552887Z", + "shell.execute_reply": "2024-10-03T09:53:34.552339Z" } }, "outputs": [], @@ -857,10 +857,10 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.366951Z", - "iopub.status.busy": "2024-10-01T10:21:35.366563Z", - "iopub.status.idle": "2024-10-01T10:21:35.369997Z", - "shell.execute_reply": "2024-10-01T10:21:35.369425Z" + "iopub.execute_input": "2024-10-03T09:53:34.554719Z", + "iopub.status.busy": "2024-10-03T09:53:34.554520Z", + "iopub.status.idle": "2024-10-03T09:53:34.558319Z", + "shell.execute_reply": "2024-10-03T09:53:34.557763Z" } }, "outputs": [ @@ -897,10 +897,10 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:35.372058Z", - "iopub.status.busy": "2024-10-01T10:21:35.371676Z", - "iopub.status.idle": "2024-10-01T10:21:35.376989Z", - "shell.execute_reply": "2024-10-01T10:21:35.376400Z" + "iopub.execute_input": "2024-10-03T09:53:34.560117Z", + "iopub.status.busy": "2024-10-03T09:53:34.559940Z", + "iopub.status.idle": "2024-10-03T09:53:34.565394Z", + "shell.execute_reply": "2024-10-03T09:53:34.564851Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-conductance.ipynb b/notebooks/nmodl-sympy-conductance.ipynb index a09e3e83b..471a11f7f 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": "2024-10-01T10:21:37.821174Z", - "iopub.status.busy": "2024-10-01T10:21:37.820574Z", - "iopub.status.idle": "2024-10-01T10:21:38.618818Z", - "shell.execute_reply": "2024-10-01T10:21:38.617989Z" + "iopub.execute_input": "2024-10-03T09:53:37.029702Z", + "iopub.status.busy": "2024-10-03T09:53:37.029512Z", + "iopub.status.idle": "2024-10-03T09:53:37.826943Z", + "shell.execute_reply": "2024-10-03T09:53:37.826135Z" } }, "outputs": [], @@ -103,10 +103,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.621301Z", - "iopub.status.busy": "2024-10-01T10:21:38.621084Z", - "iopub.status.idle": "2024-10-01T10:21:38.651744Z", - "shell.execute_reply": "2024-10-01T10:21:38.651083Z" + "iopub.execute_input": "2024-10-03T09:53:37.829354Z", + "iopub.status.busy": "2024-10-03T09:53:37.829140Z", + "iopub.status.idle": "2024-10-03T09:53:37.859411Z", + "shell.execute_reply": "2024-10-03T09:53:37.858638Z" } }, "outputs": [], @@ -149,10 +149,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.654226Z", - "iopub.status.busy": "2024-10-01T10:21:38.653834Z", - "iopub.status.idle": "2024-10-01T10:21:38.931262Z", - "shell.execute_reply": "2024-10-01T10:21:38.930514Z" + "iopub.execute_input": "2024-10-03T09:53:37.861808Z", + "iopub.status.busy": "2024-10-03T09:53:37.861481Z", + "iopub.status.idle": "2024-10-03T09:53:38.135604Z", + "shell.execute_reply": "2024-10-03T09:53:38.134960Z" } }, "outputs": [ @@ -196,10 +196,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:38.933516Z", - "iopub.status.busy": "2024-10-01T10:21:38.933264Z", - "iopub.status.idle": "2024-10-01T10:21:39.065959Z", - "shell.execute_reply": "2024-10-01T10:21:39.065329Z" + "iopub.execute_input": "2024-10-03T09:53:38.137950Z", + "iopub.status.busy": "2024-10-03T09:53:38.137502Z", + "iopub.status.idle": "2024-10-03T09:53:38.269859Z", + "shell.execute_reply": "2024-10-03T09:53:38.269248Z" } }, "outputs": [ @@ -243,10 +243,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.068045Z", - "iopub.status.busy": "2024-10-01T10:21:39.067838Z", - "iopub.status.idle": "2024-10-01T10:21:39.076495Z", - "shell.execute_reply": "2024-10-01T10:21:39.075931Z" + "iopub.execute_input": "2024-10-03T09:53:38.272256Z", + "iopub.status.busy": "2024-10-03T09:53:38.271871Z", + "iopub.status.idle": "2024-10-03T09:53:38.280375Z", + "shell.execute_reply": "2024-10-03T09:53:38.279751Z" } }, "outputs": [ @@ -290,10 +290,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.078383Z", - "iopub.status.busy": "2024-10-01T10:21:39.078181Z", - "iopub.status.idle": "2024-10-01T10:21:39.095112Z", - "shell.execute_reply": "2024-10-01T10:21:39.094537Z" + "iopub.execute_input": "2024-10-03T09:53:38.282442Z", + "iopub.status.busy": "2024-10-03T09:53:38.281980Z", + "iopub.status.idle": "2024-10-03T09:53:38.299215Z", + "shell.execute_reply": "2024-10-03T09:53:38.298551Z" } }, "outputs": [ @@ -337,10 +337,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.097092Z", - "iopub.status.busy": "2024-10-01T10:21:39.096877Z", - "iopub.status.idle": "2024-10-01T10:21:39.215347Z", - "shell.execute_reply": "2024-10-01T10:21:39.214752Z" + "iopub.execute_input": "2024-10-03T09:53:38.301612Z", + "iopub.status.busy": "2024-10-03T09:53:38.301136Z", + "iopub.status.idle": "2024-10-03T09:53:38.419523Z", + "shell.execute_reply": "2024-10-03T09:53:38.418841Z" } }, "outputs": [ @@ -400,10 +400,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.217531Z", - "iopub.status.busy": "2024-10-01T10:21:39.217320Z", - "iopub.status.idle": "2024-10-01T10:21:39.313393Z", - "shell.execute_reply": "2024-10-01T10:21:39.312662Z" + "iopub.execute_input": "2024-10-03T09:53:38.421923Z", + "iopub.status.busy": "2024-10-03T09:53:38.421414Z", + "iopub.status.idle": "2024-10-03T09:53:38.515903Z", + "shell.execute_reply": "2024-10-03T09:53:38.515301Z" } }, "outputs": [ @@ -456,10 +456,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:39.315719Z", - "iopub.status.busy": "2024-10-01T10:21:39.315219Z", - "iopub.status.idle": "2024-10-01T10:21:39.388710Z", - "shell.execute_reply": "2024-10-01T10:21:39.387983Z" + "iopub.execute_input": "2024-10-03T09:53:38.518071Z", + "iopub.status.busy": "2024-10-03T09:53:38.517679Z", + "iopub.status.idle": "2024-10-03T09:53:38.591539Z", + "shell.execute_reply": "2024-10-03T09:53:38.590857Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-solver-cnexp.ipynb b/notebooks/nmodl-sympy-solver-cnexp.ipynb index bec37eafb..9841e393f 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": "2024-10-01T10:21:41.326725Z", - "iopub.status.busy": "2024-10-01T10:21:41.326155Z", - "iopub.status.idle": "2024-10-01T10:21:42.137111Z", - "shell.execute_reply": "2024-10-01T10:21:42.136334Z" + "iopub.execute_input": "2024-10-03T09:53:40.365376Z", + "iopub.status.busy": "2024-10-03T09:53:40.364829Z", + "iopub.status.idle": "2024-10-03T09:53:41.156781Z", + "shell.execute_reply": "2024-10-03T09:53:41.155887Z" } }, "outputs": [], @@ -79,10 +79,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.139932Z", - "iopub.status.busy": "2024-10-01T10:21:42.139501Z", - "iopub.status.idle": "2024-10-01T10:21:42.170809Z", - "shell.execute_reply": "2024-10-01T10:21:42.170151Z" + "iopub.execute_input": "2024-10-03T09:53:41.159607Z", + "iopub.status.busy": "2024-10-03T09:53:41.159193Z", + "iopub.status.idle": "2024-10-03T09:53:41.190016Z", + "shell.execute_reply": "2024-10-03T09:53:41.189404Z" } }, "outputs": [], @@ -123,10 +123,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.173320Z", - "iopub.status.busy": "2024-10-01T10:21:42.172853Z", - "iopub.status.idle": "2024-10-01T10:21:42.610616Z", - "shell.execute_reply": "2024-10-01T10:21:42.609890Z" + "iopub.execute_input": "2024-10-03T09:53:41.192396Z", + "iopub.status.busy": "2024-10-03T09:53:41.191997Z", + "iopub.status.idle": "2024-10-03T09:53:41.609066Z", + "shell.execute_reply": "2024-10-03T09:53:41.608387Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.612789Z", - "iopub.status.busy": "2024-10-01T10:21:42.612376Z", - "iopub.status.idle": "2024-10-01T10:21:42.726609Z", - "shell.execute_reply": "2024-10-01T10:21:42.725883Z" + "iopub.execute_input": "2024-10-03T09:53:41.611297Z", + "iopub.status.busy": "2024-10-03T09:53:41.610852Z", + "iopub.status.idle": "2024-10-03T09:53:41.722451Z", + "shell.execute_reply": "2024-10-03T09:53:41.721774Z" } }, "outputs": [ @@ -207,10 +207,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.728917Z", - "iopub.status.busy": "2024-10-01T10:21:42.728504Z", - "iopub.status.idle": "2024-10-01T10:21:42.929400Z", - "shell.execute_reply": "2024-10-01T10:21:42.928749Z" + "iopub.execute_input": "2024-10-03T09:53:41.724817Z", + "iopub.status.busy": "2024-10-03T09:53:41.724390Z", + "iopub.status.idle": "2024-10-03T09:53:41.924048Z", + "shell.execute_reply": "2024-10-03T09:53:41.923429Z" } }, "outputs": [ @@ -255,10 +255,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:42.931679Z", - "iopub.status.busy": "2024-10-01T10:21:42.931276Z", - "iopub.status.idle": "2024-10-01T10:21:43.092553Z", - "shell.execute_reply": "2024-10-01T10:21:43.091899Z" + "iopub.execute_input": "2024-10-03T09:53:41.926283Z", + "iopub.status.busy": "2024-10-03T09:53:41.925871Z", + "iopub.status.idle": "2024-10-03T09:53:42.084576Z", + "shell.execute_reply": "2024-10-03T09:53:42.083899Z" } }, "outputs": [ @@ -303,10 +303,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T10:21:43.094821Z", - "iopub.status.busy": "2024-10-01T10:21:43.094408Z", - "iopub.status.idle": "2024-10-01T10:21:44.860368Z", - "shell.execute_reply": "2024-10-01T10:21:44.859636Z" + "iopub.execute_input": "2024-10-03T09:53:42.086953Z", + "iopub.status.busy": "2024-10-03T09:53:42.086545Z", + "iopub.status.idle": "2024-10-03T09:53:43.836453Z", + "shell.execute_reply": "2024-10-03T09:53:43.835742Z" } }, "outputs": [ @@ -351,10 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