Replace links with refs #406
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orbeckst
requested changes
Mar 24, 2025
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The PR does what it says – fixes the ever-broken links. ✅
The notebook tests themselves fail after ~8 mins and do not leave anything in the logs except "Error" everywhere. However, when I watch them, they start up and start testing. From the open browser window I got the output below.
@lilyminium @RMeli what's the best way forward?
nbtesting
============================= test session starts ==============================
platform linux -- Python 3.10.16, pytest-8.3.5, pluggy-1.5.0
rootdir: /home/runner/work/UserGuide/UserGuide/tests
configfile: pytest.ini
testpaths: ../doc/source/examples/analysis/volumetric/, ../doc/source/examples/analysis/custom_parallel_analysis.ipynb, ../doc/source/examples/analysis/custom_trajectory_analysis.ipynb, ../doc/source/examples/constructing_universe.ipynb, ../doc/source/examples/quickstart.ipynb, ../doc/source/examples/analysis/distances_and_contacts/, ../doc/source/examples/analysis/alignment_and_rms, ../doc/source/examples/analysis/distances_and_contacts/, ../doc/source/examples/analysis/hydrogen_bonds/, ../doc/source/examples/analysis/polymers_and_membranes/, ../doc/source/examples/analysis/reduced_dimensions/, ../doc/source/examples/analysis/structure/, ../doc/source/examples/analysis/trajectory_similarity/, ../doc/source/examples/transformations/, ../doc/source/examples/other/
plugins: nbval-0.11.0, syrupy-4.9.0, hypothesis-6.130.2, anyio-4.9.0
collected 602 items
density_analysis.ipynb ...................s... [ 3%]
linear_density.ipynb ......... [ 5%]
. ...................................................................... [ 10%]
............................................................... [ 11%]
contacts_custom.ipynb ....... [ 13%]
contacts_native_fraction.ipynb .................... [ 16%]
contacts_q1q2.ipynb ...... [ 17%]
contacts_within_cutoff.ipynb ....... [ 18%]
distances_between_atomgroups.ipynb ....... [ 19%]
distances_between_selections.ipynb ........ [ 21%]
distances_within_selection.ipynb ........... [ 22%]
aligning_structure_to_another.ipynb .............. [ 25%]
aligning_trajectory.ipynb ................ [ 27%]
aligning_trajectory_to_frame.ipynb ......... [ 29%]
pairwise_rmsd.ipynb ......... [ 30%]
rmsd.ipynb ............... [ 33%]
rmsf.ipynb ............. [ 35%]
hbonds-lifetimes.ipynb ................... [ 38%]
hbonds-selections.ipynb ........... [ 40%]
hbonds.ipynb .......................... [ 44%]
hole2.ipynb .FFFFFFFFFFFFFFFFFFFFF.FFFFFFFFF [ 50%]
polymer.ipynb ........ [ 51%]
diffusion_map.ipynb ........ [ 52%]
pca.ipynb ................. [ 55%]
average_rdf.ipynb .............. [ 57%]
dihedrals.ipynb ............. [ 60%]
elastic_network.ipynb ........... [ 61%]
helanal.ipynb .......... [ 63%]
site_specific_rdf.ipynb .............. [ 65%]
clustering_ensemble_similarity.ipynb ..................... [ 69%]
convergence.ipynb .............. [ 71%]
dimension_reduction_ensemble_similarity.ipynb ....................... [ 75%]
harmonic_ensemble_similarity.ipynb ....... [ 76%]
psa.ipynb ...FFFFFFFFF [ 78%]
center_protein_in_box.ipynb .............. [ 81%]
parmed_sim.ipynb ..................... [ 84%]
=================================== FAILURES ===================================
___________________________________ ::Cell 1 ___________________________________
Notebook cell execution failed
Cell 1: Cell execution caused an exception
Input:
profiles = hole2.hole(PDB_HOLE,
outfile='hole1.out',
sphpdb_file='hole1.sph',
vdwradii_file=None,
random_seed=31415,
# executable='~/hole2/exe/hole',
)
Traceback:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[1], line 1
----> 1 profiles = hole2.hole(PDB_HOLE,
2 outfile='hole1.out',
3 sphpdb_file='hole1.sph',
4 vdwradii_file=None,
5 random_seed=31415,
6 # executable='~/hole2/exe/hole',
7 )
AttributeError: module 'MDAnalysis.analysis.hole2' has no attribute 'hole'
___________________________________ ::Cell 2 ___________________________________
Notebook cell execution failed
Cell 2: Cell execution caused an exception
Input:
profiles[0].shape
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 profiles[0].shape
NameError: name 'profiles' is not defined
___________________________________ ::Cell 3 ___________________________________
Notebook cell execution failed
Cell 3: Cell execution caused an exception
Input:
profiles[0].dtype.names
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 profiles[0].dtype.names
NameError: name 'profiles' is not defined
___________________________________ ::Cell 4 ___________________________________
Notebook cell execution failed
Cell 4: Cell execution caused an exception
Input:
rxn_coords = profiles[0].rxn_coord
pore_length = rxn_coords[-1] - rxn_coords[0]
print('The pore is {} angstroms long'.format(pore_length))
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 rxn_coords = profiles[0].rxn_coord
2 pore_length = rxn_coords[-1] - rxn_coords[0]
3 print('The pore is {} angstroms long'.format(pore_length))
NameError: name 'profiles' is not defined
___________________________________ ::Cell 5 ___________________________________
Notebook cell execution failed
Cell 5: Cell execution caused an exception
Input:
hole2.create_vmd_surface(filename='hole1.vmd',
sphpdb='hole1.sph',
# sph_process='~/hole2/exe/sph_process',
)
Traceback:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[1], line 1
----> 1 hole2.create_vmd_surface(filename='hole1.vmd',
2 sphpdb='hole1.sph',
3 # sph_process='~/hole2/exe/sph_process',
4 )
AttributeError: module 'MDAnalysis.analysis.hole2' has no attribute 'create_vmd_surface'
___________________________________ ::Cell 6 ___________________________________
Notebook cell execution failed
Cell 6: Cell execution caused an exception
Input:
from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
u = mda.Universe(MULTIPDB_HOLE)
ha = hole2.HoleAnalysis(u, select='protein',
cpoint='center_of_geometry',
# executable='~/hole2/exe/hole',
)
ha.run(random_seed=31415)
Traceback:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[1], line 5
1 from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
3 u = mda.Universe(MULTIPDB_HOLE)
----> 5 ha = hole2.HoleAnalysis(u, select='protein',
6 cpoint='center_of_geometry',
7 # executable='~/hole2/exe/hole',
8 )
9 ha.run(random_seed=31415)
AttributeError: module 'MDAnalysis.analysis.hole2' has no attribute 'HoleAnalysis'
___________________________________ ::Cell 7 ___________________________________
Notebook cell execution failed
Cell 7: Cell execution caused an exception
Input:
for rxn_coord, radius, cen_line_D in (ha.results.profiles[3][:10]):
print(f"{rxn_coord:.2f}, {radius:.2f}, {cen_line_D:.2f}")
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 for rxn_coord, radius, cen_line_D in (ha.results.profiles[3][:10]):
2 print(f"{rxn_coord:.2f}, {radius:.2f}, {cen_line_D:.2f}")
NameError: name 'ha' is not defined
___________________________________ ::Cell 8 ___________________________________
Notebook cell execution failed
Cell 8: Cell execution caused an exception
Input:
gathered = ha.gather()
print(gathered.keys())
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 gathered = ha.gather()
2 print(gathered.keys())
NameError: name 'ha' is not defined
___________________________________ ::Cell 9 ___________________________________
Notebook cell execution failed
Cell 9: Cell execution caused an exception
Input:
print(len(gathered['rxn_coord']))
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 print(len(gathered['rxn_coord']))
NameError: name 'gathered' is not defined
__________________________________ ::Cell 10 ___________________________________
Notebook cell execution failed
Cell 10: Cell execution caused an exception
Input:
flat = ha.gather(flat=True)
print(len(flat['rxn_coord']))
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 flat = ha.gather(flat=True)
2 print(len(flat['rxn_coord']))
NameError: name 'ha' is not defined
__________________________________ ::Cell 11 ___________________________________
Notebook cell execution failed
Cell 11: Cell execution caused an exception
Input:
radii, edges = ha.bin_radii(bins=100, range=None)
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 radii, edges = ha.bin_radii(bins=100, range=None)
NameError: name 'ha' is not defined
__________________________________ ::Cell 12 ___________________________________
Notebook cell execution failed
Cell 12: Cell execution caused an exception
Input:
means, edges = ha.histogram_radii(bins=100, range=None,
aggregator=np.mean)
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 means, edges = ha.histogram_radii(bins=100, range=None,
2 aggregator=np.mean)
NameError: name 'ha' is not defined
__________________________________ ::Cell 13 ___________________________________
Notebook cell execution failed
Cell 13: Cell execution caused an exception
Input:
midpoints = 0.5*(edges[1:]+edges[:-1])
plt.plot(midpoints, means)
plt.ylabel(r"Mean HOLE radius $R$ ($\AA$)")
plt.xlabel(r"Pore coordinate $\zeta$ ($\AA$)")
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 midpoints = 0.5*(edges[1:]+edges[:-1])
2 plt.plot(midpoints, means)
3 plt.ylabel(r"Mean HOLE radius $R$ ($\AA$)")
NameError: name 'edges' is not defined
__________________________________ ::Cell 14 ___________________________________
Notebook cell execution failed
Cell 14: Cell execution caused an exception
Input:
min_radii = ha.min_radius()
for frame, min_radius in min_radii:
print(f"Frame {int(frame)}: {min_radius:.3f}")
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 min_radii = ha.min_radius()
2 for frame, min_radius in min_radii:
3 print(f"Frame {int(frame)}: {min_radius:.3f}")
NameError: name 'ha' is not defined
__________________________________ ::Cell 15 ___________________________________
Notebook cell execution failed
Cell 15: Cell execution caused an exception
Input:
plt.plot(min_radii[:, 0], min_radii[:, 1])
plt.ylabel('Minimum HOLE radius $R$ ($\AA$)')
plt.xlabel('Frame')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 plt.plot(min_radii[:, 0], min_radii[:, 1])
2 plt.ylabel('Minimum HOLE radius $R$ ($\AA$)')
3 plt.xlabel('Frame')
NameError: name 'min_radii' is not defined
__________________________________ ::Cell 16 ___________________________________
Notebook cell execution failed
Cell 16: Cell execution caused an exception
Input:
ha.create_vmd_surface(filename='holeanalysis.vmd')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.create_vmd_surface(filename='holeanalysis.vmd')
NameError: name 'ha' is not defined
__________________________________ ::Cell 17 ___________________________________
Notebook cell execution failed
Cell 17: Cell execution caused an exception
Input:
ha.plot()
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot()
NameError: name 'ha' is not defined
__________________________________ ::Cell 18 ___________________________________
Notebook cell execution failed
Cell 18: Cell execution caused an exception
Input:
ha.plot(frames=[0, 2, 5, 9])
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot(frames=[0, 2, 5, 9])
NameError: name 'ha' is not defined
__________________________________ ::Cell 19 ___________________________________
Notebook cell execution failed
Cell 19: Cell execution caused an exception
Input:
ha.plot3D()
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot3D()
NameError: name 'ha' is not defined
__________________________________ ::Cell 20 ___________________________________
Notebook cell execution failed
Cell 20: Cell execution caused an exception
Input:
ha.plot3D(r_max=2.5)
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot3D(r_max=2.5)
NameError: name 'ha' is not defined
__________________________________ ::Cell 21 ___________________________________
Notebook cell execution failed
Cell 21: Cell execution caused an exception
Input:
ha.plot_mean_profile(bins=100, # how much to chunk rxn_coord
n_std=1, # how many standard deviations from mean
color='blue', # color of plot
fill_alpha=0.2, # opacity of standard deviation
legend=True)
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot_mean_profile(bins=100, # how much to chunk rxn_coord
2 n_std=1, # how many standard deviations from mean
3 color='blue', # color of plot
4 fill_alpha=0.2, # opacity of standard deviation
5 legend=True)
NameError: name 'ha' is not defined
__________________________________ ::Cell 23 ___________________________________
Notebook cell execution failed
Cell 23: Cell execution caused an exception
Input:
op_profiles = ha.over_order_parameters(rmsd_values)
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 op_profiles = ha.over_order_parameters(rmsd_values)
NameError: name 'ha' is not defined
__________________________________ ::Cell 24 ___________________________________
Notebook cell execution failed
Cell 24: Cell execution caused an exception
Input:
for order_parameter, profile in op_profiles.items():
print(f"{order_parameter:.3f}, {len(profile)}")
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 for order_parameter, profile in op_profiles.items():
2 print(f"{order_parameter:.3f}, {len(profile)}")
NameError: name 'op_profiles' is not defined
__________________________________ ::Cell 25 ___________________________________
Notebook cell execution failed
Cell 25: Cell execution caused an exception
Input:
op_profiles = ha.over_order_parameters(rmsd_values, frames=[0, 4, 9])
for order_parameter, profile in op_profiles.items():
print(f"{order_parameter:.3f}, {len(profile)}")
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 op_profiles = ha.over_order_parameters(rmsd_values, frames=[0, 4, 9])
2 for order_parameter, profile in op_profiles.items():
3 print(f"{order_parameter:.3f}, {len(profile)}")
NameError: name 'ha' is not defined
__________________________________ ::Cell 26 ___________________________________
Notebook cell execution failed
Cell 26: Cell execution caused an exception
Input:
ha.plot_order_parameters(rmsd_values,
aggregator=min,
xlabel='RMSD to reference ($\AA$)',
ylabel='Minimum HOLE pore radius $r$ ($\AA$)')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot_order_parameters(rmsd_values,
2 aggregator=min,
3 xlabel='RMSD to reference ($\AA$)',
4 ylabel='Minimum HOLE pore radius $r$ ($\AA$)')
NameError: name 'ha' is not defined
__________________________________ ::Cell 27 ___________________________________
Notebook cell execution failed
Cell 27: Cell execution caused an exception
Input:
ha.plot3D_order_parameters(rmsd_values,
ylabel='RMSD to reference ($\AA$)')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.plot3D_order_parameters(rmsd_values,
2 ylabel='RMSD to reference ($\AA$)')
NameError: name 'ha' is not defined
__________________________________ ::Cell 28 ___________________________________
Notebook cell execution failed
Cell 28: Cell execution caused an exception
Input:
ha.tmp_files
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.tmp_files
NameError: name 'ha' is not defined
__________________________________ ::Cell 29 ___________________________________
Notebook cell execution failed
Cell 29: Cell execution caused an exception
Input:
ha.delete_temporary_files()
ha.tmp_files
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ha.delete_temporary_files()
2 ha.tmp_files
NameError: name 'ha' is not defined
__________________________________ ::Cell 30 ___________________________________
Notebook cell execution failed
Cell 30: Cell execution caused an exception
Input:
with hole2.HoleAnalysis(u,
# executable='~/hole2/exe/hole',
) as ha2:
ha2.run()
ha2.create_vmd_surface(filename='holeanalysis.vmd')
ha2.plot()
Traceback:
ps.run(metric='discrete_frechet')
ps.D
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 ps.run(metric='discrete_frechet')
2 ps.D
NameError: name 'ps' is not defined
__________________________________ ::Cell 10 ___________________________________
Notebook cell execution failed
Cell 10: Cell execution caused an exception
Input:
fig = ps.plot(linkage='ward')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 fig = ps.plot(linkage='ward')
NameError: name 'ps' is not defined
__________________________________ ::Cell 11 ___________________________________
Notebook cell execution failed
Cell 11: Cell execution caused an exception
Input:
fig = ps.plot_annotated_heatmap(linkage='single')
Traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[1], line 1
----> 1 fig = ps.plot_annotated_heatmap(linkage='single')
NameError: name 'ps' is not defined
=========================== short test summary info ============================
FAILED hole2.ipynb::Cell 1
FAILED hole2.ipynb::Cell 2
FAILED hole2.ipynb::Cell 3
FAILED hole2.ipynb::Cell 4
FAILED hole2.ipynb::Cell 5
FAILED hole2.ipynb::Cell 6
FAILED hole2.ipynb::Cell 7
FAILED hole2.ipynb::Cell 8
FAILED hole2.ipynb::Cell 9
FAILED hole2.ipynb::Cell 10
FAILED hole2.ipynb::Cell 11
FAILED hole2.ipynb::Cell 12
FAILED hole2.ipynb::Cell 13
FAILED hole2.ipynb::Cell 14
FAILED hole2.ipynb::Cell 15
FAILED hole2.ipynb::Cell 16
FAILED hole2.ipynb::Cell 17
FAILED hole2.ipynb::Cell 18
FAILED hole2.ipynb::Cell 19
FAILED hole2.ipynb::Cell 20
FAILED hole2.ipynb::Cell 21
FAILED hole2.ipynb::Cell 23
FAILED hole2.ipynb::Cell 24
FAILED hole2.ipynb::Cell 25
FAILED hole2.ipynb::Cell 26
FAILED hole2.ipynb::Cell 27
FAILED hole2.ipynb::Cell 28
FAILED hole2.ipynb::Cell 29
FAILED hole2.ipynb::Cell 30
FAILED hole2.ipynb::Cell 31
FAILED psa.ipynb::Cell 3
FAILED psa.ipynb::Cell 4
FAILED psa.ipynb::Cell 5
FAILED psa.ipynb::Cell 6
FAILED psa.ipynb::Cell 7
FAILED psa.ipynb::Cell 8
FAILED psa.ipynb::Cell 9
FAILED psa.ipynb::Cell 10
FAILED psa.ipynb::Cell 11
============ 39 failed, 562 passed, 1 skipped in 443.86s (0:07:23) =============
doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
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* add some preliminary guesser docs * fix ipython blocks * Apply suggestions from code review Co-authored-by: Rocco Meli <[email protected]> * link to Guesser API * Update guessing.rst - address @RMeli comments - minor grammar fixes - moved note on radii guessing to explicit rst note * Apply suggestions from code review fix whitespace to make pre-hook check happy * fix ipython block * add changes from review * add link to changelog --------- Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Rocco Meli <[email protected]>
|
Yup there were a few things breaking CI, I fixed them in earlier PRs and rebased to get CI working here. |
orbeckst
approved these changes
Mar 24, 2025
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Some RST links to notebooks don't work, likely because nbsphinx links don't work that way and they should be refs instead. Not sure if they ever worked originally or if I messed up and misread the docs 😬
Edit: for more info, the reason the nb links didn't work in both the top-level analysis/README.rst and the lower-level examples/analysis/alignment-and-rms/README.rst was that the local links struggled to resolve to two different levels.
refs get around that.📚 Documentation preview 📚: https://mdanalysisuserguide--406.org.readthedocs.build/en/406/