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Merged
RMeli merged 5 commits into from
Mar 5, 2025
Merged

Update script to strip numpy typing and re-execute notebooks #408

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04d3653
update types
lilyminium Mar 1, 2025
d76d6b5
update script instead of types
lilyminium Mar 1, 2025
bf843b0
re-execute nbs to update numpy types
lilyminium Mar 1, 2025
185cf8f
re-execute additional
lilyminium Mar 4, 2025
f062586
re-execute quickstart too
lilyminium Mar 4, 2025
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8 changes: 4 additions & 4 deletions doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
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Expand Up @@ -241,7 +241,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"(21.712154435976014, 6.817293751703919)\n"
"(np.float64(21.712154435976014), 6.817293751703919)\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"(18.991465038265208, 16.603704620787127)\n"
"(np.float64(18.991465038265208), 16.603704620787127)\n"
]
}
],
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"metadata": {
"celltoolbar": "Raw Cell Format",
"kernelspec": {
"display_name": "Python 3.9.15 ('mda-user-guide')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -502,7 +502,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.10.16"
},
"toc": {
"base_numbering": 1,
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197 changes: 140 additions & 57 deletions doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb
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35 changes: 17 additions & 18 deletions doc/source/examples/analysis/structure/dihedrals.ipynb
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22 changes: 10 additions & 12 deletions doc/source/examples/analysis/structure/site_specific_rdf.ipynb
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66 changes: 27 additions & 39 deletions doc/source/examples/analysis/trajectory_similarity/harmonic_ensemble_similarity.ipynb
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Expand Up @@ -49,7 +49,17 @@
"shell.execute_reply": "2021-05-19T06:01:12.662787Z"
}
},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0\n",
"MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0.\n",
" warnings.warn(wmsg, category=DeprecationWarning)\n"
]
}
],
"source": [
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
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"name": "stderr",
"output_type": "stream",
"text": [
"/home/pbarletta/mambaforge/envs/mda-user-guide/lib/python3.9/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behaviour will be changed in 3.0 to be the same as other readers\n",
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.\n",
" warnings.warn(\"DCDReader currently makes independent timesteps\"\n"
]
}
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"shell.execute_reply": "2021-05-19T06:03:04.424122Z"
}
},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911\n",
" warnings.warn(\n"
]
}
],
"source": [
"hes, details = encore.hes([u1, u2, u3, u4],\n",
" select='backbone',\n",
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"name": "stdout",
"output_type": "stream",
"text": [
" 0.0 24955.7 1879874.5 145622.3 \n",
" 0.0 24955.7 1879874.9 145622.3 \n",
" 24955.7 0.0 1659867.5 161102.3 \n",
" 1879874.5 1659867.5 0.0 9900092.7 \n",
" 145622.3 161102.3 9900092.7 0.0 \n"
" 1879874.9 1659867.5 0.0 9900093.4 \n",
" 145622.3 161102.3 9900093.4 0.0 \n"
]
}
],
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"\n",
"[4] Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. *J Mol Biol*. 2009;394(1):160–176. [doi:10.1016/j.jmb.2009.09.009](https://dx.doi.org/10.1016%2Fj.jmb.2009.09.009)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## References\n",
"\n",
"[1] Oliver Beckstein, Elizabeth&nbsp;J. Denning, Juan&nbsp;R. Perilla, and Thomas&nbsp;B. Woolf.\n",
"Zipping and <span class=\"bibtex-protected\">Unzipping</span> of <span class=\"bibtex-protected\">Adenylate</span> <span class=\"bibtex-protected\">Kinase</span>: <span class=\"bibtex-protected\">Atomistic</span> <span class=\"bibtex-protected\">Insights</span> into the <span class=\"bibtex-protected\">Ensemble</span> of <span class=\"bibtex-protected\">Open</span>↔<span class=\"bibtex-protected\">Closed</span> <span class=\"bibtex-protected\">Transitions</span>.\n",
"<em>Journal of Molecular Biology</em>, 394(1):160–176, November 2009.\n",
"00107.\n",
"URL: <a href=\"https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164\">https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164</a>, <a href=\"https://doi.org/10.1016/j.jmb.2009.09.009\">doi:10.1016/j.jmb.2009.09.009</a>.\n",
"\n",
"[2] Richard&nbsp;J. Gowers, Max Linke, Jonathan Barnoud, Tyler J.&nbsp;E. Reddy, Manuel&nbsp;N. Melo, Sean&nbsp;L. Seyler, Jan Domański, David&nbsp;L. Dotson, Sébastien Buchoux, Ian&nbsp;M. Kenney, and Oliver Beckstein.\n",
"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> <span class=\"bibtex-protected\">Python</span> <span class=\"bibtex-protected\">Package</span> for the <span class=\"bibtex-protected\">Rapid</span> <span class=\"bibtex-protected\">Analysis</span> of <span class=\"bibtex-protected\">Molecular</span> <span class=\"bibtex-protected\">Dynamics</span> <span class=\"bibtex-protected\">Simulations</span>.\n",
"<em>Proceedings of the 15th Python in Science Conference</em>, pages 98–105, 2016.\n",
"00152.\n",
"URL: <a href=\"https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html\">https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html</a>, <a href=\"https://doi.org/10.25080/Majora-629e541a-00e\">doi:10.25080/Majora-629e541a-00e</a>.\n",
"\n",
"[3] Naveen Michaud-Agrawal, Elizabeth&nbsp;J. Denning, Thomas&nbsp;B. Woolf, and Oliver Beckstein.\n",
"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> toolkit for the analysis of molecular dynamics simulations.\n",
"<em>Journal of Computational Chemistry</em>, 32(10):2319–2327, July 2011.\n",
"00778.\n",
"URL: <a href=\"http://doi.wiley.com/10.1002/jcc.21787\">http://doi.wiley.com/10.1002/jcc.21787</a>, <a href=\"https://doi.org/10.1002/jcc.21787\">doi:10.1002/jcc.21787</a>.\n",
"\n",
"[4] Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen.\n",
"<span class=\"bibtex-protected\">ENCORE</span>: <span class=\"bibtex-protected\">Software</span> for <span class=\"bibtex-protected\">Quantitative</span> <span class=\"bibtex-protected\">Ensemble</span> <span class=\"bibtex-protected\">Comparison</span>.\n",
"<em>PLOS Computational Biology</em>, 11(10):e1004415, October 2015.\n",
"00031.\n",
"URL: <a href=\"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415\">https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415</a>, <a href=\"https://doi.org/10.1371/journal.pcbi.1004415\">doi:10.1371/journal.pcbi.1004415</a>."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.9.15 ('mda-user-guide')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -371,7 +359,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.10.16"
},
"toc": {
"base_numbering": 1,
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299 changes: 250 additions & 49 deletions doc/source/examples/analysis/volumetric/linear_density.ipynb
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22 changes: 12 additions & 10 deletions doc/source/examples/constructing_universe.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"Using MDAnalysis version 2.6.0-dev0\n"
"Using MDAnalysis version 2.9.0-dev0\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "1177615fa88e496c827928276bc1fc63",
"model_id": "a7825c7b10e04802b0859664fd854a83",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -57,7 +57,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Using NGLView version 3.0.3\n"
"Using NGLView version 3.0.8\n"
]
}
],
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{
"data": {
"text/plain": [
"array(['O', 'H1', 'H2', ..., 'O', 'H1', 'H2'], dtype=object)"
"array(['O', 'H1', 'H2', ..., 'O', 'H1', 'H2'], shape=(3000,), dtype=object)"
]
},
"execution_count": 4,
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{
"data": {
"text/plain": [
"array(['O', 'H', 'H', ..., 'O', 'H', 'H'], dtype=object)"
"array(['O', 'H', 'H', ..., 'O', 'H', 'H'], shape=(3000,), dtype=object)"
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},
"execution_count": 5,
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{
"data": {
"text/plain": [
"array(['SOL', 'SOL', 'SOL', ..., 'SOL', 'SOL', 'SOL'], dtype=object)"
"array(['SOL', 'SOL', 'SOL', ..., 'SOL', 'SOL', 'SOL'],\n",
" shape=(3000,), dtype=object)"
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{
"data": {
"text/plain": [
"array([ 1, 1, 1, ..., 1000, 1000, 1000])"
"array([ 1, 1, 1, ..., 1000, 1000, 1000], shape=(3000,))"
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{
"data": {
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"array(['SOL', 'SOL', 'SOL', ..., 'SOL', 'SOL', 'SOL'], dtype=object)"
"array(['SOL', 'SOL', 'SOL', ..., 'SOL', 'SOL', 'SOL'],\n",
" shape=(3000,), dtype=object)"
]
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"execution_count": 8,
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{
"data": {
"text/plain": [
"73.23912"
"np.float32(73.23912)"
]
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"execution_count": 33,
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.2"
"version": "3.10.16"
},
"toc": {
"base_numbering": 1,
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12 changes: 6 additions & 6 deletions doc/source/examples/quickstart.ipynb
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2 changes: 1 addition & 1 deletion doc/source/scripts/gen_topologyattr_defaults.py
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Expand Up @@ -33,7 +33,7 @@ def _default(klass: TopologyAttr) -> str:
return DEFAULTS[klass.attrname]
except KeyError:
try:
return repr(klass._gen_initial_values(1, 1, 1)[0])
return repr(klass._gen_initial_values(1, 1, 1).tolist()[0])
except NotImplementedError:
return "No default values"

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