timestep #4447
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timestep #4447
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Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.
Linter Bot Results:Hi @nataliyah123! Thanks for making this PR. We linted your code and found the following: There are currently no issues detected! 🎉 |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4447 +/- ##
===========================================
- Coverage 93.69% 93.63% -0.06%
===========================================
Files 168 180 +12
Lines 21215 22294 +1079
Branches 3913 3908 -5
===========================================
+ Hits 19877 20875 +998
- Misses 886 961 +75
- Partials 452 458 +6 ☔ View full report in Codecov by Sentry. |
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@hmacdope could you please look after this PR? Either review yourself or find reviewers. Thanks. |
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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.
or if we want to keep it simple and fictitious only then we can query like |
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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? |
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@nataliyah123 I am just asking @hmacdope to manage the PR, i.e., making sure it gets reviewed and hopefully eventually merged. |
thanks |
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Hi @nataliyah123! Welcome to MDAnalysis and thanks for the PR. I will try and answer some of your questions below.
Timestep is not deprecated, it serves a different purpose to
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
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.
Running doctest on your branch, you need to keep working on the test to make it work. I use the command From within the Personally I wouldn't bother with the Hope this helps! You are on the right track. :) |
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@hmacdope. The |
hmacdope
requested changes
Feb 19, 2024
| >>> ts_1.dimensions | ||
| array([80.13008, 80.13008, 80.13008, 60. , 60. , 90. ], dtype=float32) | ||
| >>> ts_1.triclinic_dimensions | ||
| array([[80.13008 , 0. , 0. ], |
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You made some progress, but now the doctest if failing on comparison with this array, try and reduce the precision of the comparison. Have a detailed look at the output of make doctest to see if your changes are working
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@hmacdope . I rounded the values. it does reflect in doctest.
Results of doctest builder run on 2024-02-20 09:17:35
=====================================================
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:
{('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>, ('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>}
**********************************************************************
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/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/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/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/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/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.
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/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/coordinates/timestep
--------------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
ts.dimensions
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>
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/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>
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.
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/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/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.
Doctest summary
===============
508 tests
66 failures in tests
2 failures in setup code
0 failures in cleanup code
hmacdope
requested changes
Feb 20, 2024
There was a problem hiding this comment.
Still having trouble with the imports
Document: documentation_pages/coordinates/timestep
--------------------------------------------------
**********************************************************************
File "None", line ?, in default
Failed example:
ts.dimensions
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>
ts.dimensions
^^
NameError: name 'ts' is not defined
```
|
@hmacdope sorry it was 'does not reflect' instead of 'does reflect'. |
|
@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, |
IAlibay
requested changes
Mar 10, 2024
There was a problem hiding this comment.
@nataliyah123 could you please add yourself to AUTHORS and the CHANGELOG developers list?
|
Also please tick this box - this needs to be done before we can merge anything. |
IAlibay
requested changes
Mar 11, 2024
package/AUTHORS
Outdated
Comment on lines
236
to
237
|
|
||
| 2024 |
There was a problem hiding this comment.
Suggested change
| 2024 | |
| 2024 |
Just need to revert this back to the previous formatting.
There was a problem hiding this comment.
@IAlibay all the rest of the years in the Authors file do not have any space except for 2024 which has two spaces, I have aligned the year 2024 with the rest of the years, if you still want me to revert the changes, I will do that.
There was a problem hiding this comment.
Sorry @nataliyah123 I don't think I fully understand what you mean. The image above (of the 2022 entry) is how it should look for 2024. My suggested change should fix things to how they should be.
There was a problem hiding this comment.
@IAlibay made the changes you suggested in both files. and reverted the changes you asked. I was talking about the spaces as shown in the image below.
|
@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). |
|
@IAlibay. sorry I have not checked the html version before the push. now after the changes I made when I run |
|
mdahole2 is added approx 2 weeks ago. hole2 was deprecated not removed. So, the question is there should I install or not? |
|
@hmacdope can you please take over on this? @nataliyah123 - briefly yes, you need to install mdahole2. |
|
@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 <<<<<<<<<<<<<<<<<<<<<<
environment variables: populated config files : An unexpected error has occurred. Conda has prepared the above report. Example: conda --no-plugins install Alternatively, you can set the CONDA_NO_PLUGINS environment variable on Example: CONDA_NO_PLUGINS=true conda install If submitted, this report will be used by core maintainers to improve No report sent. To permanently opt-out, use |
|
I have installed hole2. |
orbeckst
requested changes
Mar 29, 2024
| @@ -62,7 +62,7 @@ Deprecations | |||
|
|
|||
| 12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, | |||
| richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya, | |||
| JoStoe, jennaswa, ljwoods2 | |||
| JoStoe, jennaswa, ljwoods2, SumairaAhmad | |||
There was a problem hiding this comment.
You would put your GitHub handle here — nataliyah123
| @@ -236,6 +236,7 @@ Chronological list of authors | |||
| 2024 | |||
| - Aditya Keshari | |||
| - Philipp Stärk | |||
| - SumairaAhmad | |||
There was a problem hiding this comment.
Most contributors put their real name here, which typically contains spaces. But you can also put your GitHub handle here if you do not want to put your real name. In this case it would be nataliyah123 as far as I can tell.
Comment on lines
+498
to
+502
| >>> import MDAnalysis as mda | ||
| >>> from MDAnalysis.tests.datafiles import TPR, XTC | ||
| >>> import numpy as np | ||
| >>> u = mda.Universe(TPR, XTC) | ||
| >>> ts = u.trajectory[0] |
There was a problem hiding this comment.
Based on a similar PR https://github.com/MDAnalysis/mdanalysis/pull/4374/files these lines should be indented to look like
.. testsetup::
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import TPR, XTC
...
and I am not 100% sure if >>> should remain.
|
|
||
| .. doctest:: | ||
|
|
||
| >>> print(np.round(ts.dimensions)) |
|
|
||
| .. doctest:: | ||
|
|
||
| >>> print(np.round(ts.dimensions)) |
There was a problem hiding this comment.
Is rounding really required? It makes for less clear documentation. I'd like to get rid of it if at all possible so that it does not distract from what we are really interested in, namely ts.dimensions. The documentation aspect is more important than the testing...
| array([ 15. , 15.81138802, 16.58312416, 67.58049774, | ||
| 72.45159912, 71.56504822], dtype=float32) | ||
|
|
||
| >>> print(np.round(ts.dimensions)) |
There was a problem hiding this comment.
rounding here just gives the wrong output. Find a way to do this without round.
There was a problem hiding this comment.
@orbeckst I am getting this 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
I think mdahole2 uses python 3.11 or less I am using 3.12 so I am unable to install mdahole2. please check the error report I have attached in an earlier message. I will make the requested changes once this is resolved
There was a problem hiding this comment.
You might have to install in a Python 3.11 environment for testing. The development version is a work in progress and even though we strive to make it fully usable, this is not always possible until close to a release.
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Partially addresses #3925
Changes made in this Pull Request:
PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4447.org.readthedocs.build/en/4447/