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Partially addresses #3925

Changes made in this Pull Request:

added few lines to make docstring in timestep.pyx work

PR Checklist

[ ] Tests?
[ ] Docs?
[ ] CHANGELOG updated?
[ ] Issue raised/referenced?

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📚 Documentation preview 📚: https://mdanalysis--4447.org.readthedocs.build/en/4447/

Feb 03 '24 06:02 nataliyah123

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Feb 03 '24 06:02 github-actions[bot]

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@@             Coverage Diff             @@
##           develop    #4447      +/-   ##
===========================================
- Coverage    93.69%   93.63%   -0.06%     
===========================================
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  Lines        21215    22294    +1079     
  Branches      3913     3908       -5     
===========================================
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Feb 03 '24 06:02 codecov[bot]

@hmacdope could you please look after this PR? Either review yourself or find reviewers. Thanks.

Feb 10 '24 01:02 orbeckst

hi @orbeckst have you assigned this PR to @hmacdope to work on this or just review and provide feedback? I think I may be wrong so please correct me if any of the following in incorrect.

timestep is deprecated and now use atom or universe
the below code or something similar should be used in testsetup for the doctest to pass.

import MDAnalysis as mda
import numpy as np

n_atoms = 100
n_frames = 100

u = mda.Universe.empty(n_atoms=n_atoms,
                       n_residues=n_atoms,
                       n_segments=n_atoms,
                       atom_resindex=np.arange(n_atoms),
                       residue_segindex=np.arange(n_atoms))

for attr in ["charges", "masses"]:
    u.add_TopologyAttr(attr, values=np.ones(n_atoms))

shape = (n_frames, n_atoms, 3)
coords = np.random.random(shape)

u.trajectory = get_reader_for(coords)(coords,
                                      order='fac',
                                      n_atoms=n_atoms)

for ts in u.trajectory:
    ts.dimensions = np.array([1, 1, 1, 90, 90, 90])

or if we want to keep it simple and fictitious

import MDAnalysis as mda
import numpy as np
rstate = np.random.RandomState(1178083)
unitcells = rstate.uniform(high=80, size=(98, 6)).astype(np.float64)
ts.dimensions = np.r_[unitcells, [90., 90., 90.]]

only then we can query like ts.dimensions . one more thing is this representation [unitcells, [90., 90., 90.]] (square brackets around the angles) correct or this [1, 1, 1, 90, 90, 90] or both are correct.

Feb 10 '24 14:02 nataliyah123

I tried to run make doctest with and without the sphinx directives but I think cython will not pass this test. Am I right? the failures were down to 67 from 69 but ts not defined errors were still there. beside the failure, I think the examples are displaying as was intended in the documents?

Feb 10 '24 14:02 nataliyah123

@nataliyah123 I am just asking @hmacdope to manage the PR, i.e., making sure it gets reviewed and hopefully eventually merged.

Feb 10 '24 22:02 orbeckst

@nataliyah123 I am just asking @hmacdope to manage the PR, i.e., making sure it gets reviewed and hopefully eventually merged.

thanks

Feb 11 '24 04:02 nataliyah123

Hi @nataliyah123! Welcome to MDAnalysis and thanks for the PR. I will try and answer some of your questions below.

timestep is deprecated and now use atom or universe

Timestep is not deprecated, it serves a different purpose to Universe (ties everything together) or AtomGroup (manages groups of atoms). Timestep is designed to contain all the trajectory data at one point in time. I would recommend trying a few of the examples in the Userguide: https://userguide.mdanalysis.org/stable/examples/README.html to get a feel for this.

the below code or something similar should be used in testsetup for the doctest to pass.

import MDAnalysis as mda
import numpy as np

n_atoms = 100
n_frames = 100

u = mda.Universe.empty(n_atoms=n_atoms,
                       n_residues=n_atoms,
                       n_segments=n_atoms,
                       atom_resindex=np.arange(n_atoms),
                       residue_segindex=np.arange(n_atoms))

for attr in ["charges", "masses"]:
    u.add_TopologyAttr(attr, values=np.ones(n_atoms))

shape = (n_frames, n_atoms, 3)
coords = np.random.random(shape)

u.trajectory = get_reader_for(coords)(coords,
                                      order='fac',
                                      n_atoms=n_atoms)

for ts in u.trajectory:
    ts.dimensions = np.array([1, 1, 1, 90, 90, 90])

or if we want to keep it simple and fictitious

import MDAnalysis as mda
import numpy as np
rstate = np.random.RandomState(1178083)
unitcells = rstate.uniform(high=80, size=(98, 6)).astype(np.float64)
ts.dimensions = np.r_[unitcells, [90., 90., 90.]]

This is roughly correct in that you will need to fully set up the example with the correct imports etc. I would use some of the MDAnalysisTests datafiles for examples such as is done here: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/analysis/msd.py#L87C1-L90C1

only then we can query like ts.dimensions . one more thing is this representation [unitcells, [90., 90., 90.]] (square brackets around the angles) correct or this [1, 1, 1, 90, 90, 90] or both are correct.

I would just make the box explicitly with [1,1,1,90,90,90] where boxes are of the form [a,b,c,x,y,z] where a, b and c are edge lengths and x, y and z are angles between cell basis vectors.

I tried to run make doctest with and without the sphinx directives but I think cython will not pass this test. Am I right? the failures were down to 67 from 69 but ts not defined errors were still there. beside the failure, I think the examples are displaying as was intended in the documents?

Running doctest on your branch, you need to keep working on the test to make it work. I use the command

sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html  | grep timestep -B 20 -A 100

From within the package directory and I am still getting the two timestep errors.

Document: documentation_pages/coordinates/timestep
--------------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
    ts.dimensions
Exception raised:
    Traceback (most recent call last):
      File "/home/hmacdope/mambaforge/envs/mdanalysis_docs/lib/python3.10/doctest.py", line 1350, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        ts.dimensions
    NameError: name 'ts' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    ts.triclinic_dimensions
Exception raised:
    Traceback (most recent call last):
      File "/home/hmacdope/mambaforge/envs/mdanalysis_docs/lib/python3.10/doctest.py", line 1350, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[1]>", line 1, in <module>
        ts.triclinic_dimensions
    NameError: name 'ts' is not defined
**********************************************************************
1 items had failures:
   2 of   2 in default
2 tests in 1 items.
0 passed and 2 failed.
***Test Failed*** 2 failures.

Personally I wouldn't bother with the .. testsetup:: blocks, but just set it up directly in the example eg

>>> from MDAnalysis.timestep import Timestep
>>> ts.dimensions
etc

Hope this helps! You are on the right track. :)

Feb 12 '24 22:02 hmacdope

@hmacdope. The make doctest will fail because of cythonization. In the last I have changed the ts to ts_1 and the test still complains about the ts. please have a look at the PR whenever you have time and let me know if it is correct or not.

Feb 17 '24 11:02 nataliyah123

@hmacdope sorry it was 'does not reflect' instead of 'does reflect'.

Feb 20 '24 11:02 nataliyah123

@hmacdope. I deleted the timestep.cpython-312-x86_64-linux-gnu.so file, recompiled the timestep.pyx using stepup.py in the package, and the new changes were reflected in the file. however, whoever has the old timestep.cpython-312-x86_64-linux-gnu.so in coordinates folder, make doctest will not show any change. Can you please also review my other PR #4458. Below is the output of the make doctest


Results of doctest builder run on 2024-02-22 20:39:17
=====================================================

Document: documentation_pages/lib/formats/libmdaxdr
---------------------------------------------------
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.TRRFile", line 18, in default
Failed example:
    with TRRFile('foo.trr') as f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[1]>", line 1
        with TRRFile('foo.trr') as f:
                                     ^
    IndentationError: expected an indented block after 'with' statement on line 1
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.TRRFile", line 19, in default
Failed example:
        for frame in f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[2]>", line 1
        for frame in f:
    IndentationError: unexpected indent
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.TRRFile", line 20, in default
Failed example:
            print(frame.x)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[3]>", line 1
        print(frame.x)
    IndentationError: unexpected indent
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.XTCFile", line 18, in default
Failed example:
    with XTCFile('foo.trr') as f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[1]>", line 1
        with XTCFile('foo.trr') as f:
                                     ^
    IndentationError: expected an indented block after 'with' statement on line 1
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.XTCFile", line 19, in default
Failed example:
        for frame in f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[2]>", line 1
        for frame in f:
    IndentationError: unexpected indent
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libmdaxdr.XTCFile", line 20, in default
Failed example:
            print(frame.x)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[3]>", line 1
        print(frame.x)
    IndentationError: unexpected indent
**********************************************************************
1 items had failures:
   6 of   8 in default
8 tests in 1 items.
2 passed and 6 failed.
***Test Failed*** 6 failures.

Document: documentation_pages/core/groups
-----------------------------------------
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag2.ix
Expected:
    array([2, 1, 0], dtype=int64)
Got:
    array([2, 1, 0])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag3.ix
Expected:
    array([0, 1, 2], dtype=int64)
Got:
    array([0, 1, 2])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    u.atoms[[2, 1, 1, 0, 1]].asunique(sorted=False).ix
Expected:
    array([2, 1, 0], dtype=int64)
Got:
    array([2, 1, 0])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag.groupby('masses')
Expected:
    {12.010999999999999: <AtomGroup with 462 atoms>,
     14.007: <AtomGroup with 116 atoms>,
     15.999000000000001: <AtomGroup with 134 atoms>}
Got:
    {1.008: <AtomGroup with 2 atoms>, 14.007: <AtomGroup with 1 atom>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])
Expected:
    {('ALA', 1.008): <AtomGroup with 95 atoms>,
     ('ALA', 12.011): <AtomGroup with 57 atoms>,
     ('ALA', 14.007): <AtomGroup with 19 atoms>,
     ('ALA', 15.999): <AtomGroup with 19 atoms>},
     ('ARG', 1.008): <AtomGroup with 169 atoms>,
     ...}
Got:
    {('MET', 1.008): <AtomGroup with 2 atoms>, ('MET', 14.007): <AtomGroup with 1 atom>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])('ALA', 15.999)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        ag.groupby(['resnames', 'masses'])('ALA', 15.999)
    TypeError: 'dict' object is not callable
**********************************************************************
File "None", line ?, in default
Failed example:
    sel = universe.select_atoms('resname MET GLY')
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        sel = universe.select_atoms('resname MET GLY')
              ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    sel = universe.select_atoms('resname MET or resname GLY')
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        sel = universe.select_atoms('resname MET or resname GLY')
              ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    sel = universe.select_atoms("segid DMPC and not ( name H* O* )")
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        sel = universe.select_atoms("segid DMPC and not ( name H* O* )")
              ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    sel
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[1]>", line 1, in <module>
        sel
    NameError: name 'sel' is not defined. Did you mean: 'set'?
**********************************************************************
File "None", line ?, in default
Failed example:
    universe.select_atoms("around 10 group notHO", notHO=sel)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        universe.select_atoms("around 10 group notHO", notHO=sel)
        ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    universe.select_atoms("resname SOL and around 2.0 protein", updating=True)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        universe.select_atoms("resname SOL and around 2.0 protein", updating=True)
        ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    universe.select_atoms("C", smarts_kwargs={"maxMatches": 100})
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        universe.select_atoms("C", smarts_kwargs={"maxMatches": 100})
        ^^^^^^^^
    NameError: name 'universe' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag1.indices
Expected:
    array([3, 3, 1, 1])
Got:
    array([3, 3, 2, 2, 1, 1])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag3.indices  # 0 and 1 are only in ag1, 4 and 6 are only in ag2
Expected:
    [0, 1, 4, 6]
Got:
    array([0, 1, 4, 6])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag.ix
Expected:
    array([2, 1, 2, 2, 1, 0], dtype=int64)
Got:
    array([2, 1, 2, 2, 1, 0])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag2.ix
Expected:
    array([0, 1, 2], dtype=int64)
Got:
    array([0, 1, 2])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    rg2.ix
Expected:
    array([0, 1, 2])
Got:
    array([2, 1, 0])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag.groupby('masses')
Expected:
    {12.010999999999999: <AtomGroup with 462 atoms>,
     14.007: <AtomGroup with 116 atoms>,
     15.999000000000001: <AtomGroup with 134 atoms>}
Got:
    {32.06: <AtomGroup with 7 atoms>, 1.008: <AtomGroup with 1685 atoms>, 12.011: <AtomGroup with 1040 atoms>, 14.007: <AtomGroup with 289 atoms>, 15.999: <AtomGroup with 320 atoms>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])
Expected:
    {('ALA', 1.008): <AtomGroup with 95 atoms>,
     ('ALA', 12.011): <AtomGroup with 57 atoms>,
     ('ALA', 14.007): <AtomGroup with 19 atoms>,
     ('ALA', 15.999): <AtomGroup with 19 atoms>},
     ('ARG', 1.008): <AtomGroup with 169 atoms>,
     ...}
Got:
    {('THR', 1.008): <AtomGroup with 77 atoms>, ('THR', 12.011): <AtomGroup with 44 atoms>, ('THR', 14.007): <AtomGroup with 11 atoms>, ('THR', 15.999): <AtomGroup with 22 atoms>, ('MET', 32.06): <AtomGroup with 6 atoms>, ('MET', 1.008): <AtomGroup with 56 atoms>, ('MET', 12.011): <AtomGroup with 30 atoms>, ('MET', 14.007): <AtomGroup with 6 atoms>, ('MET', 15.999): <AtomGroup with 6 atoms>, ('ALA', 1.008): <AtomGroup with 95 atoms>, ('ALA', 12.011): <AtomGroup with 57 atoms>, ('ALA', 14.007): <AtomGroup with 19 atoms>, ('ALA', 15.999): <AtomGroup with 19 atoms>, ('GLY', 1.008): <AtomGroup with 60 atoms>, ('GLY', 12.011): <AtomGroup with 40 atoms>, ('GLY', 14.007): <AtomGroup with 20 atoms>, ('GLY', 15.999): <AtomGroup with 21 atoms>, ('SER', 1.008): <AtomGroup with 25 atoms>, ('SER', 12.011): <AtomGroup with 15 atoms>, ('SER', 14.007): <AtomGroup with 5 atoms>, ('SER', 15.999): <AtomGroup with 10 atoms>, ('ASP', 1.008): <AtomGroup with 68 atoms>, ('ASP', 12.011): <AtomGroup with 68 atoms>, ('ASP', 14.007): <AtomGroup with 17 atoms>, ('ASP', 15.999): <AtomGroup with 51 atoms>, ('CYS', 32.06): <AtomGroup with 1 atom>, ('CYS', 1.008): <AtomGroup with 5 atoms>, ('CYS', 12.011): <AtomGroup with 3 atoms>, ('CYS', 14.007): <AtomGroup with 1 atom>, ('CYS', 15.999): <AtomGroup with 1 atom>, ('ASN', 1.008): <AtomGroup with 24 atoms>, ('ASN', 12.011): <AtomGroup with 16 atoms>, ('ASN', 14.007): <AtomGroup with 8 atoms>, ('ASN', 15.999): <AtomGroup with 8 atoms>, ('LEU', 1.008): <AtomGroup with 176 atoms>, ('LEU', 12.011): <AtomGroup with 96 atoms>, ('LEU', 14.007): <AtomGroup with 16 atoms>, ('LEU', 15.999): <AtomGroup with 16 atoms>, ('PHE', 1.008): <AtomGroup with 45 atoms>, ('PHE', 12.011): <AtomGroup with 45 atoms>, ('PHE', 14.007): <AtomGroup with 5 atoms>, ('PHE', 15.999): <AtomGroup with 5 atoms>, ('GLN', 1.008): <AtomGroup with 64 atoms>, ('GLN', 12.011): <AtomGroup with 40 atoms>, ('GLN', 14.007): <AtomGroup with 16 atoms>, ('GLN', 15.999): <AtomGroup with 16 atoms>, ('GLU', 1.008): <AtomGroup with 108 atoms>, ('GLU', 12.011): <AtomGroup with 90 atoms>, ('GLU', 14.007): <AtomGroup with 18 atoms>, ('GLU', 15.999): <AtomGroup with 54 atoms>, ('PRO', 1.008): <AtomGroup with 70 atoms>, ('PRO', 12.011): <AtomGroup with 50 atoms>, ('PRO', 14.007): <AtomGroup with 10 atoms>, ('PRO', 15.999): <AtomGroup with 10 atoms>, ('TYR', 1.008): <AtomGroup with 63 atoms>, ('TYR', 12.011): <AtomGroup with 63 atoms>, ('TYR', 14.007): <AtomGroup with 7 atoms>, ('TYR', 15.999): <AtomGroup with 14 atoms>, ('ILE', 1.008): <AtomGroup with 154 atoms>, ('ILE', 12.011): <AtomGroup with 84 atoms>, ('ILE', 14.007): <AtomGroup with 14 atoms>, ('ILE', 15.999): <AtomGroup with 14 atoms>, ('LYS', 1.008): <AtomGroup with 234 atoms>, ('LYS', 12.011): <AtomGroup with 108 atoms>, ('LYS', 14.007): <AtomGroup with 36 atoms>, ('LYS', 15.999): <AtomGroup with 18 atoms>, ('HSD', 1.008): <AtomGroup with 21 atoms>, ('HSD', 12.011): <AtomGroup with 18 atoms>, ('HSD', 14.007): <AtomGroup with 9 atoms>, ('HSD', 15.999): <AtomGroup with 3 atoms>, ('VAL', 1.008): <AtomGroup with 171 atoms>, ('VAL', 12.011): <AtomGroup with 95 atoms>, ('VAL', 14.007): <AtomGroup with 19 atoms>, ('VAL', 15.999): <AtomGroup with 19 atoms>, ('ARG', 1.008): <AtomGroup with 169 atoms>, ('ARG', 12.011): <AtomGroup with 78 atoms>, ('ARG', 14.007): <AtomGroup with 52 atoms>, ('ARG', 15.999): <AtomGroup with 13 atoms>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])('ALA', 15.999)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        ag.groupby(['resnames', 'masses'])('ALA', 15.999)
    TypeError: 'dict' object is not callable
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag1.indices
Expected:
    array([3, 3, 1, 1])
Got:
    array([3, 3, 2, 2, 1, 1])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag3.indices  # 0 and 1 are only in ag1, 4 and 6 are only in ag2
Expected:
    [0, 1, 4, 6]
Got:
    array([0, 1, 4, 6])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg = u.segments[[2, 1, 2, 2, 1, 0]]
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        sg = u.segments[[2, 1, 2, 2, 1, 0]]
             ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
      File "/mnt/c/Users/sumairaibiA/code/mdanalysis/mdanalysis/package/MDAnalysis/core/groups.py", line 601, in __getitem__
        return self._derived_class(self.ix[item], self.universe)
                                   ~~~~~~~^^^^^^
    IndexError: index 2 is out of bounds for axis 0 with size 1
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[1]>", line 1, in <module>
        sg
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg.ix
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[2]>", line 1, in <module>
        sg.ix
        ^^
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2 = sg.asunique()
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[3]>", line 1, in <module>
        sg2 = sg.asunique()
              ^^
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[4]>", line 1, in <module>
        sg2
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2.ix
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[5]>", line 1, in <module>
        sg2.ix
        ^^^
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2.asunique() is sg2
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[6]>", line 1, in <module>
        sg2.asunique() is sg2
        ^^^
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag.groupby('masses')
Expected:
    {12.010999999999999: <AtomGroup with 462 atoms>,
     14.007: <AtomGroup with 116 atoms>,
     15.999000000000001: <AtomGroup with 134 atoms>}
Got:
    {1.008: <AtomGroup with 5 atoms>, 14.007: <AtomGroup with 1 atom>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])
Expected:
    {('ALA', 1.008): <AtomGroup with 95 atoms>,
     ('ALA', 12.011): <AtomGroup with 57 atoms>,
     ('ALA', 14.007): <AtomGroup with 19 atoms>,
     ('ALA', 15.999): <AtomGroup with 19 atoms>},
     ('ARG', 1.008): <AtomGroup with 169 atoms>,
     ...}
Got:
    {('MET', 1.008): <AtomGroup with 5 atoms>, ('MET', 14.007): <AtomGroup with 1 atom>}
**********************************************************************
File "None", line ?, in default
Failed example:
    ag.groupby(['resnames', 'masses'])('ALA', 15.999)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        ag.groupby(['resnames', 'masses'])('ALA', 15.999)
    TypeError: 'dict' object is not callable
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag1.indices
Expected:
    array([3, 3, 1, 1])
Got:
    array([3, 3, 2, 2, 1, 1])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    ag3.indices  # 0 and 1 are only in ag1, 4 and 6 are only in ag2
Expected:
    [0, 1, 4, 6]
Got:
    array([0, 1, 4, 6])
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg = u.segments[[2, 1, 2, 2, 1, 0]]
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        sg = u.segments[[2, 1, 2, 2, 1, 0]]
             ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
      File "/mnt/c/Users/sumairaibiA/code/mdanalysis/mdanalysis/package/MDAnalysis/core/groups.py", line 601, in __getitem__
        return self._derived_class(self.ix[item], self.universe)
                                   ~~~~~~~^^^^^^
    IndexError: index 2 is out of bounds for axis 0 with size 1
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[1]>", line 1, in <module>
        sg
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg.ix
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[2]>", line 1, in <module>
        sg.ix
        ^^
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2 = sg.unique
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[3]>", line 1, in <module>
        sg2 = sg.unique
              ^^
    NameError: name 'sg' is not defined
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[4]>", line 1, in <module>
        sg2
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2.ix
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[5]>", line 1, in <module>
        sg2.ix
        ^^^
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
File "../../../MDAnalysis/core/groups.py", line ?, in default
Failed example:
    sg2.unique is sg2
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[6]>", line 1, in <module>
        sg2.unique is sg2
        ^^^
    NameError: name 'sg2' is not defined. Did you mean: 'ag2'?
**********************************************************************
1 items had failures:
  42 of 148 in default
148 tests in 1 items.
106 passed and 42 failed.
***Test Failed*** 42 failures.

Document: documentation_pages/analysis/base
-------------------------------------------
1 items passed all tests:
   8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.

Document: documentation_pages/core/topology
-------------------------------------------
1 items passed all tests:
   5 tests in default
5 tests in 1 items.
5 passed and 0 failed.
Test passed.

Document: documentation_pages/analysis/pca
------------------------------------------
**********************************************************************
File "../../../MDAnalysis/analysis/pca.py", line ?, in default (setup code)
Failed example:
    >>> import MDAnalysis as mda
    >>> import MDAnalysis.analysis.pca as pca
    >>> from MDAnalysis.tests.datafiles import PSF, DCD
    >>> u = mda.Universe(PSF, DCD)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default (setup code)[0]>", line 1
        >>> import MDAnalysis as mda
        ^^
    SyntaxError: invalid syntax
**********************************************************************
File "../../../MDAnalysis/analysis/pca.py", line ?, in default (setup code)
Failed example:
    >>> import MDAnalysis as mda
    >>> import MDAnalysis.analysis.pca as pca
    >>> from MDAnalysis.tests.datafiles import PSF, DCD
    >>> u = mda.Universe(PSF, DCD)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default (setup code)[1]>", line 1
        >>> import MDAnalysis as mda
        ^^
    SyntaxError: invalid syntax
**********************************************************************
1 items had failures:
   2 of   2 in default (setup code)
***Test Failed*** 2 failures.

Document: documentation_pages/coordinates/timestep
--------------------------------------------------
1 items passed all tests:
   7 tests in default
7 tests in 1 items.
7 passed and 0 failed.
Test passed.

Document: documentation_pages/analysis/encore/similarity
--------------------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
    print(HES)
Expected:
    [[       0.         38279540.04524205]
     [38279540.04524205        0.        ]]
Got:
    [[       0.        38279535.2809184]
     [38279535.2809184        0.       ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(HES)
Expected:
    [[       0.         38279540.04524205]
     [38279540.04524205        0.        ]]
Got:
    [[       0.        38279535.2809184]
     [38279535.2809184        0.       ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(encore.hes([ens1, ens2], align=True)[0])
Expected:
    [[   0.         6889.89729056]
     [6889.89729056    0.        ]]
Got:
    [[   0.         6889.89687843]
     [6889.89687843    0.        ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(encore.hes([ens1, ens2])[0])
Expected:
    [[   0.         6889.89729056]
     [6889.89729056    0.        ]]
Got:
    [[   0.         6889.89687843]
     [6889.89687843    0.        ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(HES)
Expected:
    [[       0.         38279540.04524205]
     [38279540.04524205        0.        ]]
Got:
    [[       0.        38279535.2809184]
     [38279535.2809184        0.       ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(encore.hes([ens1, ens2], align=True)[0])
Expected:
    [[   0.         6889.89729056]
     [6889.89729056    0.        ]]
Got:
    [[   0.         6889.89687843]
     [6889.89687843    0.        ]]
**********************************************************************
File "None", line ?, in default
Failed example:
    print(encore.hes([ens1, ens2])[0])
Expected:
    [[   0.         6889.89729056]
     [6889.89729056    0.        ]]
Got:
    [[   0.         6889.89687843]
     [6889.89687843    0.        ]]
**********************************************************************
1 items had failures:
   7 of 102 in default
102 tests in 1 items.
95 passed and 7 failed.
***Test Failed*** 7 failures.

Document: documentation_pages/lib/transformations
-------------------------------------------------
1 items passed all tests:
 160 tests in default
160 tests in 1 items.
160 passed and 0 failed.
Test passed.

Document: documentation_pages/lib/formats/libdcd
------------------------------------------------
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libdcd.DCDFile", line 24, in default
Failed example:
    with DCDFile('foo.dcd') as f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[1]>", line 1
        with DCDFile('foo.dcd') as f:
                                     ^
    IndentationError: expected an indented block after 'with' statement on line 1
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libdcd.DCDFile", line 25, in default
Failed example:
        for frame in f:
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[2]>", line 1
        for frame in f:
    IndentationError: unexpected indent
**********************************************************************
File "../docstring of MDAnalysis.lib.formats.libdcd.DCDFile", line 26, in default
Failed example:
            print(frame.x)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/site-packages/sphinx/ext/doctest.py", line 484, in compile
        return compile(code, name, self.type, flags, dont_inherit)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<doctest default[3]>", line 1
        print(frame.x)
    IndentationError: unexpected indent
**********************************************************************
1 items had failures:
   3 of   4 in default
4 tests in 1 items.
1 passed and 3 failed.
***Test Failed*** 3 failures.

Document: documentation_pages/analysis/align
--------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
    rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions, center=True)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions, center=True)
        ^^^^
    NameError: name 'rmsd' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions,
         superposition=True)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions,
        ^^^^
    NameError: name 'rmsd' is not defined
**********************************************************************
1 items had failures:
   2 of   2 in default
2 tests in 1 items.
0 passed and 2 failed.
***Test Failed*** 2 failures.

Document: documentation_pages/core/universe
-------------------------------------------
1 items passed all tests:
  24 tests in default
24 tests in 1 items.
24 passed and 0 failed.
Test passed.

Document: documentation_pages/analysis/rms
------------------------------------------
1 items passed all tests:
   9 tests in default
9 tests in 1 items.
9 passed and 0 failed.
Test passed.

Document: documentation_pages/coordinates/LAMMPS
------------------------------------------------
**********************************************************************
File "../../../MDAnalysis/coordinates/LAMMPS.py", line ?, in default
Failed example:
    for ts in u.trajectory:
        # analyze frame
        if take_this_frame == True:
            with mda.Writer('frame.data') as W:
                W.write(u.atoms)
            break
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        for ts in u.trajectory:
                  ^
    NameError: name 'u' is not defined
**********************************************************************
1 items had failures:
   1 of   1 in default
1 tests in 1 items.
0 passed and 1 failed.
***Test Failed*** 1 failures.

Document: documentation_pages/lib/util
--------------------------------------
1 items passed all tests:
  30 tests in default
30 tests in 1 items.
30 passed and 0 failed.
Test passed.

Document: documentation_pages/converters/OpenMM
-----------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
    import openmm.app as app
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[0]>", line 1, in <module>
        import openmm.app as app
    ModuleNotFoundError: No module named 'openmm'
**********************************************************************
File "None", line ?, in default
Failed example:
    pdbxfile = app.PDBxFile(PDBX)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[3]>", line 1, in <module>
        pdbxfile = app.PDBxFile(PDBX)
                   ^^^
    NameError: name 'app' is not defined
**********************************************************************
File "None", line ?, in default
Failed example:
    mda.Universe(pdbxfile)
Exception raised:
    Traceback (most recent call last):
      File "/home/ibia/anaconda3/envs/mdanalysis-dev/lib/python3.12/doctest.py", line 1359, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest default[4]>", line 1, in <module>
        mda.Universe(pdbxfile)
                     ^^^^^^^^
    NameError: name 'pdbxfile' is not defined
**********************************************************************
1 items had failures:
   3 of   5 in default
5 tests in 1 items.
2 passed and 3 failed.
***Test Failed*** 3 failures.

Doctest summary
===============
  513 tests
   64 failures in tests
    2 failures in setup code
    0 failures in cleanup code

Feb 22 '24 16:02 nataliyah123

Also please tick this box - this needs to be done before we can merge anything.

Mar 10 '24 17:03 IAlibay

@hmacdope - my things have been addressed, but it looks like the page render isn't doing what's intended? https://mdanalysis--4447.org.readthedocs.build/en/4447/documentation_pages/coordinates/timestep.html

Since you approved it, could you just double check that this is what you intend? (please feel free to dismiss my blocking review if that is the case).

Mar 12 '24 17:03 IAlibay

@IAlibay. sorry I have not checked the html version before the push. now after the changes I made when I run make html. I am getting the following error autodoc: failed to import module 'hole2' from module 'MDAnalysis.analysis'; the following exception was raised: No module named 'mdahole2' make: *** [Makefile:130: doctest] Error 2 do you know how to resolve this?

Mar 13 '24 12:03 nataliyah123

@IAlibay. I have tried python setup.py build_ext --inplace as was suggested in the documents. but the error is still there. Now I found this doc, so my question is do I need to install mdahole2 in order to get rid of this error. I know hole 2 is deprecated in 2.8.0.

Mar 16 '24 12:03 nataliyah123

mdahole2 is added approx 2 weeks ago. hole2 was deprecated not removed. So, the question is there should I install or not?

Mar 19 '24 13:03 nataliyah123

@hmacdope can you please take over on this?

@nataliyah123 - briefly yes, you need to install mdahole2.

Mar 19 '24 16:03 IAlibay

@hmacdope. I am using python version 3.12 and followed the instruction here didn't use environment.yml . and I got the following error. I think it is trying to find the package in python 3.11. `

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 898, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/common/io.py", line 85, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/plan.py", line 528, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 138, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 199, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
    out_state = self._solving_loop(in_state, out_state, index)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
    solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 426, in _solve_attempt
    new_conflicts = self._maybe_raise_for_problems(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 713, in _maybe_raise_for_problems
    self._maybe_raise_for_conda_build(
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 831, in _maybe_raise_for_conda_build
    raise exc
conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("hole2"), MatchSpec("mdanalysis")}
Encountered problems while solving:
  - nothing provides requested hole2
  - nothing provides requested mdanalysis

Could not solve for environment specs
The following packages are incompatible
├─ hole2 does not exist (perhaps a typo or a missing channel);
└─ mdanalysis does not exist (perhaps a typo or a missing channel).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 898, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/common/io.py", line 85, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/plan.py", line 528, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 138, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 199, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
    out_state = self._solving_loop(in_state, out_state, index)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
    solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 426, in _solve_attempt
    new_conflicts = self._maybe_raise_for_problems(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 713, in _maybe_raise_for_problems
    self._maybe_raise_for_conda_build(
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 831, in _maybe_raise_for_conda_build
    raise exc
conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("hole2"), MatchSpec("mdanalysis")}
Encountered problems while solving:
  - nothing provides requested hole2
  - nothing provides requested mdanalysis

Could not solve for environment specs
The following packages are incompatible
├─ hole2 does not exist (perhaps a typo or a missing channel);
└─ mdanalysis does not exist (perhaps a typo or a missing channel).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 898, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/common/io.py", line 85, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/plan.py", line 528, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 138, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 199, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
    out_state = self._solving_loop(in_state, out_state, index)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
    solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 426, in _solve_attempt
    new_conflicts = self._maybe_raise_for_problems(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 713, in _maybe_raise_for_problems
    self._maybe_raise_for_conda_build(
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 831, in _maybe_raise_for_conda_build
    raise exc
conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("hole2"), MatchSpec("mdanalysis")}
Encountered problems while solving:
  - nothing provides requested hole2
  - nothing provides requested mdanalysis

Could not solve for environment specs
The following packages are incompatible
├─ hole2 does not exist (perhaps a typo or a missing channel);
└─ mdanalysis does not exist (perhaps a typo or a missing channel).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/build.py", line 3789, in build_tree
    packages_from_this = build(
                         ^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/build.py", line 2573, in build
    create_build_envs(top_level_pkg, notest)
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/build.py", line 2407, in create_build_envs
    raise e
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/build.py", line 2378, in create_build_envs
    environ.get_install_actions(
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 944, in get_install_actions
    actions = get_install_actions(
              ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 944, in get_install_actions
    actions = get_install_actions(
              ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 944, in get_install_actions
    actions = get_install_actions(
              ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/environ.py", line 898, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/common/io.py", line 85, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/plan.py", line 528, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 138, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 199, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
    out_state = self._solving_loop(in_state, out_state, index)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
    solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 426, in _solve_attempt
    new_conflicts = self._maybe_raise_for_problems(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 713, in _maybe_raise_for_problems
    self._maybe_raise_for_conda_build(
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 831, in _maybe_raise_for_conda_build
    raise exc
conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("hole2"), MatchSpec("mdanalysis")}
Encountered problems while solving:
  - nothing provides requested hole2
  - nothing provides requested mdanalysis

Could not solve for environment specs
The following packages are incompatible
├─ hole2 does not exist (perhaps a typo or a missing channel);
└─ mdanalysis does not exist (perhaps a typo or a missing channel).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 83, in main_subshell
    exit_code = do_call(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 170, in do_call
    result = plugin_subcommand.action(getattr(args, "_args", args))
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/plugin.py", line 10, in build
    execute(*args, **kwargs)
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/cli/main_build.py", line 572, in execute
    outputs = api.build(
              ^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/api.py", line 254, in build
    return build_tree(
           ^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/build.py", line 3971, in build_tree
    dep_metas = render_recipe(
                ^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/render.py", line 975, in render_recipe
    m = MetaData(recipe_dir, config=config)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/metadata.py", line 1110, in __init__
    self._meta_path = find_recipe(path)
                      ^^^^^^^^^^^^^^^^^
  File "/home/ibia/anaconda3/lib/python3.11/site-packages/conda_build/utils.py", line 1350, in find_recipe
    raise OSError(
OSError: No meta files (meta.yaml, meta.yml, conda.yaml, conda.yml) found in /mnt/c/Users/sumairaibiA/code/mdanalysis/mdanalysis

$ /home/ibia/anaconda3/bin/conda build .

environment variables: CIO_TEST= CONDA_ALLOW_SOFTLINKS=false CONDA_DEFAULT_ENV=mdanalysis-dev CONDA_EXE=/home/ibia/anaconda3/bin/conda CONDA_PREFIX=/home/ibia/anaconda3/envs/mdanalysis-dev CONDA_PREFIX_1=/home/ibia/anaconda3 CONDA_PROMPT_MODIFIER=(mdanalysis-dev) CONDA_PYTHON_EXE=/home/ibia/anaconda3/bin/python CONDA_ROOT=/home/ibia/anaconda3 CONDA_SHLVL=2 CURL_CA_BUNDLE= LD_PRELOAD= PATH=/home/ibia/.local/bin:/home/ibia/anaconda3/envs/mdanalysis-dev/bin:/ho me/ibia/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/u sr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/ Python312/Scripts:/mnt/c/Python312:/mnt/c/Windows/system32:/mnt/c/Wind ows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerS hell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt /c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1. 0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/nodejs:/mnt/c/ProgramData/chocolatey/bin:/mnt/c/Program Files/Docker/Docker/resources/bin:/mnt/c/Program Files (x86)/Microsoft Visual Studio/2022/BuildTools/MSBuild/Current/Bin:/mnt/c/Users/sumaira ibiA/.cargo/bin:/mnt/c/Users/sumairaibiA/AppData/Local/Programs/Python /Python310/Scripts:/mnt/c/Users/sumairaibiA/AppData/Local/Programs/Pyt hon/Python310:/mnt/c/Users/sumairaibiA/AppData/Local/Microsoft/Windows Apps:/mnt/c/Users/sumairaibiA/AppData/Local/Programs/Git/cmd:/mnt/c/Us ers/sumairaibiA/AppData/Roaming/npm:/mnt/c/Users/sumairaibiA/AppData/L ocal/Programs/Microsoft VS Code/bin:/snap/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : mdanalysis-dev
active env location : /home/ibia/anaconda3/envs/mdanalysis-dev
        shell level : 2
   user config file : /home/ibia/.condarc

populated config files : conda version : 23.11.0 conda-build version : 3.28.4 python version : 3.11.5.final.0 solver : libmamba (default) virtual packages : __archspec=1=skylake __conda=23.11.0=0 __cuda=12.2=0 __glibc=2.35=0 __linux=5.10.16.3=0 __unix=0=0 base environment : /home/ibia/anaconda3 (writable) conda av data dir : /home/ibia/anaconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/ibia/anaconda3/pkgs /home/ibia/.conda/pkgs envs directories : /home/ibia/anaconda3/envs /home/ibia/.conda/envs platform : linux-64 user-agent : conda/23.11.0 requests/2.31.0 CPython/3.11.5 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/22.04.2 glibc/2.35 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.6 UID:GID : 1000:1000 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

If submitted, this report will be used by core maintainers to improve future releases of conda. Would you like conda to send this report to the core maintainers? [y/N]: n

No report sent. To permanently opt-out, use

$ conda config --set report_errors false`

Mar 20 '24 08:03 nataliyah123

I have installed hole2.

Mar 20 '24 08:03 nataliyah123

mdanalysis mdanalysis copied to clipboard

timestep

PR Checklist

Developers certificate of origin

Linter Bot Results:

Codecov Report

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

mdanalysis
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