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Script interface maintenance #4482

Merged
merged 12 commits into from
Apr 4, 2022
Merged

Script interface maintenance #4482

merged 12 commits into from
Apr 4, 2022

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jngrad
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@jngrad jngrad commented Mar 29, 2022 •
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Description of changes:

  • API change: rename espressomd.reaction_ensemble to espressomd.reaction_methods
  • feature configuration: remove obsolete EXPERIMENTAL_FEATURES
  • script interface:
    • use shared pointers instead of new expressions in the script interface
    • make type conversion error messages less ambiguous by putting quotes around C++ types
    • require EK node grid indices to be exactly 3 integers (2 indices would skip the exception and return None)
  • python interface:
    • replace from X import Y by import X and X.Y in samples and python interface
    • use tqdm, numpy and f-strings more often in the samples
    • remove lj-demo.py (fixes lj-demo.py is broken #4347)
    • remove mentions to non-existent functions in the user guide

jngrad added 7 commits March 28, 2022 19:52
@jngrad
script_interface: Use shared pointers
e23f332
@jngrad
docs: Remove outdated information
8970a69
@jngrad
python: Modernize samples
f1370ec 
Use tqdm instead of print statements. Use f-strings and numpy tools
more frequently. Avoid using `from X import Y` (namespace pollution).
@jngrad
python: Cleanup import statements
8d5342b 
Replace `from X import Y` by `import X` and `X.Y` in the Cython
interface and remove unused imports.
@jngrad
python: Rename reaction_ensemble to reaction_methods
1111580
@jngrad
python: Add quotes around Python/C++ types
ef66c79
@jngrad
python: Make benchmarks deterministic
9671afc
@jngrad jngrad added this to the Espresso 4.2 milestone Mar 29, 2022
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jngrad added 2 commits March 29, 2022 02:56
@jngrad
docs: Cleanup documentation
290ed98 
Fix typos and line breaks. Remove duplicated variable types (the
System class property docstrings contain the up-to-date types).
@jngrad
samples: Remove lj-demo.py
8be90ab 
The physics is broken since release 4.0.0: logarithm input values
can be null or negative when moving the GUI sliders and the phase
diagram is incorrect. The script is also completely untested and
the NpT integrator is not properly configured.
@jngrad jngrad force-pushed the script_interface_maintenance branch from ed3e388 to 8be90ab Compare March 29, 2022 00:57
@jngrad jngrad marked this pull request as ready for review March 30, 2022 15:38
christophlohrmann
christophlohrmann previously approved these changes Apr 1, 2022
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PR seems very fine to me. One point though:
As far as I know, we need lj-demo.py for Tag der Wissenschaft. Is there anyone actively working to fix the demo?

src/python/espressomd/analyze.pyx
@@ -560,7 +559,7 @@ class Analysis:
raise ValueError("type_list_b has to be a list!")

if r_max is None:
box_l = make_array_locked(< Vector3d > box_geo.length())
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How was this never caught by anyone?

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I'm not sure, there should have been a warning about the redundant cast according to the Cython docs on type casting.

src/python/espressomd/electrokinetics.pyx Outdated Show resolved Hide resolved
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jngrad commented Apr 1, 2022

As far as I know, we need lj-demo.py for Tag der Wissenschaft. Is there anyone actively working to fix the demo?

Not that I know. I sent an email to David and Julian on March 22 to inform them of the planned removal and invite them to voice their objection, but got no reply. For the TdW event, people can use PyStar (#4382). When I used lj-demo.py for TdW 2019, people asked why the LJ simulation was following P=VNRT instead of PV=NRT, and I had no answer. The sample is broken since release 4.0.0, and unfortunately no one here was successful in implementing a working version. It is time to retire it.

@jngrad
python: Require three integers for EK node indices
d9964ec 
Also use more specific exceptions.
@jngrad jngrad requested a review from reinaual April 1, 2022 16:52
@jngrad jngrad added the automerge Merge with kodiak label Apr 4, 2022
@kodiakhq kodiakhq bot merged commit 294dcab into espressomd:python Apr 4, 2022
@jngrad jngrad deleted the script_interface_maintenance branch April 4, 2022 17:18
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@reinaual reinaual reinaual approved these changes

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lj-demo.py is broken
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