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Update docs 4.1 #3244

Merged
merged 7 commits into from
Oct 15, 2019
Merged

Update docs 4.1 #3244

merged 7 commits into from
Oct 15, 2019

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jngrad
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@jngrad jngrad commented Oct 10, 2019

Provide links to Dockerfiles, fix links in 4.1 release notes, fix typos.

jngrad added 4 commits October 10, 2019 17:55
@jngrad
Fix links in release notes
7603eb8
@jngrad
Remove duplicate argument documentation
1961cab 
Argument descriptions already in the docstrings of the linked
functions.
@jngrad
Fix typos
9fee2b9
@jngrad
Provide links to Dockerfiles for other Linux OSes
eb68e3a 
Based on feedback from the ESPResSo summer school's user and
developer meeting (@kosovan).
@jngrad jngrad added this to the Espresso 4.1.1 milestone Oct 10, 2019
@jngrad jngrad requested a review from pkreissl October 10, 2019 20:18
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codecov bot commented Oct 10, 2019 •
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Codecov Report

Merging #3244 into python will decrease coverage by <1%.
The diff coverage is n/a.

Impacted file tree graph

@@          Coverage Diff           @@
##           python   #3244   +/-   ##
======================================
- Coverage      85%     85%   -1%     
======================================
  Files         528     528           
  Lines       25805   25805           
======================================
- Hits        22150   22148    -2     
- Misses       3655    3657    +2
Impacted Files Coverage Δ
src/core/electrostatics_magnetostatics/p3m.cpp 86% <0%> (-1%) ⬇️

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jngrad commented Oct 10, 2019 •
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@christophlohrmann

  • Do you know why the first two lists of running.html#isotropic-npt-thermostat are an almost exact copy of system_setup.html#isotropic-npt-thermostat?
  • Why does system_setup.html give a circular link to itself instead of pointing to your far more detailed NPT discussion?
  • running.html says all directions fluctuate by default. Function signature says [0, 0, 0] by default. Shouldn't we write in the docstring that 0 means dimension is not fixed and 1 is fixed?
  • Why is the friction coefficient gammaV described as the piston mass Q?

    espresso/src/python/espressomd/thermostat.pyx

    Lines 429 to 431 in 9dc1e06

    gammav : :obj:`float`
    Artificial friction coefficient for the volume fluctuations.
    Mass of the artificial piston.

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codecov bot commented Oct 11, 2019 •
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Codecov Report

Merging #3244 into python will decrease coverage by <1%.
The diff coverage is n/a.

Impacted file tree graph

@@          Coverage Diff           @@
##           python   #3244   +/-   ##
======================================
- Coverage      85%     85%   -1%     
======================================
  Files         530     530           
  Lines       25795   25795           
======================================
- Hits        22168   22167    -1     
- Misses       3627    3628    +1
Impacted Files Coverage Δ
src/core/particle_data.cpp 96% <0%> (-1%) ⬇️

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@jngrad
Fix issue in the NPT documentation
823af52 
Fix broken link, incorrect docstrings and copy-paste errors (based
on inspection of the C++ code for the NPT integrator and offline
discussion with @christophlohrmann).
christophlohrmann
christophlohrmann approved these changes Oct 15, 2019
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Looks good to me

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jngrad commented Oct 15, 2019

bors r=fweik

bors bot added a commit that referenced this pull request Oct 15, 2019
@bors @jngrad @fweik
Merge #3244 #3250
94d51f5 
3244: Update docs 4.1 r=fweik a=jngrad

Provide links to Dockerfiles, fix links in 4.1 release notes, fix typos.

3250: core: virtual_sites: Removed default argument from virtual function and non-functional virtual COM feature r=jngrad a=fweik

Description of changes:
 - Removed dead code (`VIRTUAL_SITES_COM`, `THERMOSTAT_IGNORE_NON_VIRTUAL`)
 - Removed default argument on virtual function

Co-authored-by: Jean-Noël Grad <[email protected]>
Co-authored-by: Florian Weik <[email protected]>
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bors bot commented Oct 15, 2019

Build succeeded

@bors bors bot merged commit 9d95c39 into espressomd:python Oct 15, 2019
@jngrad jngrad deleted the update-docs-4.1 branch January 18, 2022 12:09
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@christophlohrmann christophlohrmann christophlohrmann approved these changes

@fweik fweik fweik approved these changes

@pkreissl pkreissl Awaiting requested review from pkreissl

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