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Get tests working again #1132

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merged 6 commits into from
Sep 15, 2023
Merged

Get tests working again #1132

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e13daad
Start getting tests working again
dwhswenson Sep 15, 2023
8aa43ef
gmx has been calver for ages now
dwhswenson Sep 15, 2023
36e68fb
hide openmm stderr from nbval
dwhswenson Sep 15, 2023
8be8a4c
guess nbval catches stderr before we redirect it
dwhswenson Sep 15, 2023
35b8ceb
Update to NEP29 (if it works?)
dwhswenson Sep 15, 2023
b70acff
Revert "Update to NEP29 (if it works?)"
dwhswenson Sep 15, 2023
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1 change: 0 additions & 1 deletion .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ jobs:
- "3.9"
- "3.8"
- "3.7"
- "2.7"
MINIMAL: [""]
include:
- CONDA_PY: "3.7"
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137 changes: 77 additions & 60 deletions examples/tests/test_openmm_integration.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,9 @@
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"from __future__ import print_function\n",
Expand All @@ -30,10 +32,25 @@
"except ImportError: # OpenMM < 7.6\n",
" import simtk.openmm as omm\n",
" import simtk.unit as u\n",
"import openmmtools as omt\n",
"\n",
"import mdtraj as md\n",
"\n",
"import openpathsampling.engines.openmm as eng\n"
"import openpathsampling.engines.openmm as eng"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_IGNORE_OUTPUT\n",
"# hide stderr from openmmtools (apparently nbval still gets it)\n",
"from os import devnull\n",
"from contextlib import redirect_stderr\n",
"\n",
"with open(devnull, 'w') as dvnl, redirect_stderr(dvnl):\n",
" import openmmtools as omt"
]
},
{
Expand All @@ -45,7 +62,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -61,7 +78,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
Expand All @@ -73,7 +90,7 @@
" '_mdtraj_topology': NoneType}"
]
},
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -111,7 +128,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -134,7 +151,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -157,7 +174,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -175,7 +192,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -194,7 +211,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -203,7 +220,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -212,35 +229,35 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[[ 0.18766736 0.11599679 0.01245004]\n",
" [ 0.19458341 0.22444927 0.00401414]\n",
" [ 0.1443672 0.27122689 0.08869714]\n",
" [ 0.14886747 0.25747473 -0.08926164]\n",
" [ 0.33994537 0.26638274 0.00609843]\n",
" [ 0.42709578 0.1897011 0.04380051]\n",
" [ 0.36886493 0.38998331 -0.03181562]\n",
" [ 0.293367 0.452431 -0.05633815]\n",
" [ 0.49859312 0.4565761 -0.02400124]\n",
" [ 0.5581438 0.41515287 0.0573552 ]\n",
" [ 0.5732535 0.43391328 -0.15561179]\n",
" [ 0.5191127 0.48312774 -0.23640657]\n",
" [ 0.67427683 0.47320502 -0.14414124]\n",
" [ 0.58423056 0.32728151 -0.17536463]\n",
" [ 0.4749522 0.60669039 -0.00127668]\n",
" [ 0.35958399 0.64924202 0.00474684]\n",
" [ 0.5835927 0.68379167 0.00902624]\n",
" [ 0.6747424 0.64066121 0.00332412]\n",
" [ 0.57127444 0.82897221 0.01853087]\n",
" [ 0.46718868 0.86095438 0.02347777]\n",
" [ 0.62214258 0.86301533 0.10872177]\n",
" [ 0.61715852 0.87434252 -0.06931573]] nm\n"
"[[ 0.18766734 0.11599676 0.01245005]\n",
" [ 0.19458354 0.22444928 0.00401417]\n",
" [ 0.14436737 0.27122667 0.08869709]\n",
" [ 0.14886761 0.25747457 -0.08926168]\n",
" [ 0.33994532 0.26638275 0.00609838]\n",
" [ 0.42709583 0.18970108 0.04380053]\n",
" [ 0.36886492 0.38998333 -0.03181563]\n",
" [ 0.29336691 0.4524309 -0.05633818]\n",
" [ 0.49859303 0.45657605 -0.02400119]\n",
" [ 0.55814379 0.41515264 0.05735509]\n",
" [ 0.57325351 0.43391326 -0.1556119 ]\n",
" [ 0.51911277 0.48312786 -0.23640618]\n",
" [ 0.67427617 0.47320503 -0.14414097]\n",
" [ 0.58423084 0.32728145 -0.17536484]\n",
" [ 0.47495231 0.60669047 -0.00127665]\n",
" [ 0.35958403 0.64924204 0.00474683]\n",
" [ 0.58359265 0.6837917 0.00902626]\n",
" [ 0.67474234 0.64066118 0.00332438]\n",
" [ 0.57127434 0.82897246 0.01853088]\n",
" [ 0.46718928 0.86095428 0.02347768]\n",
" [ 0.62214309 0.86301523 0.1087221 ]\n",
" [ 0.61715913 0.8743425 -0.06931649]] nm\n"
]
}
],
Expand All @@ -251,14 +268,14 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/sander/miniconda3/envs/python3/lib/python3.9/site-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to <class 'numpy.float32'> \n",
"/Users/dwhs/mambaforge/envs/dev/lib/python3.9/site-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to <class 'numpy.float32'> \n",
" warnings.warn(\"Casting %s dtype=%s to %s \" % (name, val.dtype, dtype),\n"
]
}
Expand All @@ -271,20 +288,20 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[ 3.1061454],\n",
" [-3.0958629],\n",
" [ 3.1367555],\n",
" [ 3.1283271],\n",
" [ 3.0931787]], dtype=float32)"
"array([[ 3.1061456],\n",
" [-3.0958636],\n",
" [ 3.136756 ],\n",
" [ 3.128327 ],\n",
" [ 3.0931773]], dtype=float32)"
]
},
"execution_count": 12,
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -296,7 +313,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -305,7 +322,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -322,7 +339,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 16,
"metadata": {},
"outputs": [
{
Expand All @@ -331,7 +348,7 @@
"'{\"_cls\":\"OpenMMEngine\",\"_dict\":{\"system_xml\":\"<?xml version=\\\\\"1.0\\\\\" ?>\\\\n<System openmmVersion=\\\\\"7.7\\\\\" type=\\\\\"System\\\\\" version=\\\\\"1\\\\\">\\\\n\\\\t<PeriodicBoxVectors>\\\\n\\\\t\\\\t<A x=\\\\\"2\\\\\" y=\\\\\"0\\\\\" z=\\\\\"0\\\\\"\\\\/>\\\\n\\\\t\\\\t<B x=\\\\\"0\\\\\" y=\\\\\"2\\\\\" z=\\\\\"0\\\\\"\\\\/>\\\\n\\\\t\\\\t<C x=\\\\\"0\\\\\" y=\\\\\"0\\\\\" z=\\\\\"2...'"
]
},
"execution_count": 15,
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -343,7 +360,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -352,7 +369,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -368,7 +385,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -377,7 +394,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -393,7 +410,7 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -402,7 +419,7 @@
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 22,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -411,7 +428,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 23,
"metadata": {},
"outputs": [
{
Expand All @@ -428,7 +445,7 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -444,7 +461,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -457,9 +474,9 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "dev",
"language": "python",
"name": "python3"
"name": "dev"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -471,7 +488,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.10"
"version": "3.9.16"
},
"toc": {
"base_numbering": 1,
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