Changelog¶
v0.9 (2025/02/19)¶
Philip Loche, Marc Sauter, Kira Fischer, Federico Grasselli, Henrik Stooß, Adyant Agrawal
Rewrite integrals in
DielectricCylinder
andDielectricSphere
to avoid numerical inaccuracies from rectangle integration method (!317)Update to Numpy 2.0 and MDAnalysis version 2.8.0 (!319)
Update virtualenv setup in CI (!316)
Split document section “Reference guide” into “Analysis Modules” and “API Documentation” (#132, !314)
Improve code quality by extending linting checks (!313)
Added tests of the analytical error propagation (!292)
Raise an error if
pack
isTrue
andrefgroup
is notNone
(!311)Use glob for find modules in docs (!312)
Distributing tests across multiple CPUs (!309)
Use Python 3.11 as default in CI (!310)
Add flag
pack
to turn off the system wrap at every frame (!308)Fix typos in
DipoleAngle
(!307)Remove handling of multiple atomgroups in favor of
AnalysisCollection
(!301)Fix openMP detection during setup (!304)
maicos.Saxs
additionally provides structure factor. (!303)Remove default arguments from core classes (!302)
Add an
AnalaysisCollection
class to perform multiple analyses on the same trajectory (!298)Remove custom module command line interface (!299)
Add example for
maicos.core.AnalysisBase
and rework own module section in developer docs (!299)Allow running an analysis with a universe without a cell (!297)
Test that
core.AnalysisBase
API andrun
method is the same asMDAnalysis.analysis.base.AnalysisBase
(!297)Add
frames
andprogressbar_kwargs
argument tomaicos.core.AnalysisBase.run()
(!297)Update copyright year (!296)
Add new diporder modules:
RDFDiporder
,DiporderStructureFactor
(!296)Add correlation time estimate for
SAXS
module (!296)Added tests of the analytical error propagation (!292)
Remove symbolic links from examples (!295)
v0.8 (2024/02/05)¶
Simon Gravelle, Philip Loche, Marc Sauter, Henrik Stooß, Philipp Staerk, Adyant Agrawal, Kira Fischer
Skip test for custom modules in case the import is not working (!294)
Change to CHANGELOG.rst update check so that it is only executed in MRs (!198)
Rename radial distribution function to pair distribution function (!278)
Add RDF derivation and explain role of dz. (!278)
Implement 1D pair distribution function in RDFCylinder (!276)
Sort format and add more atomtypes to
atomtypes.dat
(!291)Add grouping option to DipoleAngle module (!290)
Added Support for Python 3.12 (!289)
Remove suffixes
-linux
,-macos
,-windows
when building wheels. Platform will be detected automatically. (!288)Use default tox error for non-exsiting enviroment (!285)
Parse documentation metadata from
pyproject.toml
(!287)Convert
pathlib.Path
intostr
when using insys.path.append
(#123, !286)Update dev names (!284)
Improvements to documentation rendering (#122, !282)
Unify Python versions in tox environments i.e.
py311-build-macos
tobuild-macos
(!283)Remove deprecated pytest tmpdir fixture (!283)
Remove deprecated
assert_almost_equal
in favor ofassert_allclose
(!283)Move from
os.path
topathlib.Path
(!283)Added Support for Python 3.11 (!283)
Update MacOS images for CI (!281)
Removed the obsolete option for the vacuum boundary condition in the
DielectricPlanar
module and prompt users to use tin-foil boundary conditions instead (!280).Add physical integration test to test that structure factor from Saxs is the same as the Fourier transformed RDF. (!279)
Add example and explenation of how to relate the radial distribution function and the structure factor (!279)
Add function
maicos.lib.math.rdf_structure_factor()
for converting a radial distribution function into a structure factor. (!279)Change default biwnwidth (
dq
) inmaicos.Saxs
to0.1
. (!279)Move
cutils
tocmath
(!279)Add
weight
argument tomaicos.lib._cmath.compute_structure_factor()
Code cleanup of
maicos.Saxs
(!279)Fixed markup and consistency in
correlation
function docs (!277)Add info for
DielectricPlanar
module for ignored combination ofvac=True
andis_3d=False
. (!275)Add description for tox jobs (!275)
Cleanup coverage config and move to
pyproject.toml
(!275)Changed the way number normalization works, introduced sums dict (!274)
Fixed typing error in RDF modules (!273)
Update docs to reflect changes in
mdacli
(!271)Add banner to MAICoS output reporting the version (!272)
Update UML graphic (!269)
Show warnings if set boundaries would result in wrong results (!261)
Small corrections to the documentation and type hinting (!268)
Add module for calculating radial distribution functions in cylinders (!242)
Add modules for calculating cylindrical and spherical dipolar order parameters (!259)
Fix reproducibility information in output (!263)
Make savetxt work with Pathlib objects (!267)
Update versionner to 0.29 (!266)
Use
dipole_vector
methods from MDAnalysis (!265)Bump minimum Python version to 3.9 (!264)
Fix dipole calculation in
DielectricCylinder
(!258)Add example for RDFPlanar (!256)
Move geometry transformations to
lib.math
(!257)Add typehints for examples (!255)
Add typehints for modules (!253)
Only test minimum and maximum Python version in CI (!252)
Add typehints for core classes (!251)
Update documentation with parameters, returns and examples for library functions (!248)
Update CI to use latest MacOS (!250)
Add tables to documentation pages (!249)
Fix links to own classes in examples (!247)
Update install instructions for users and devs (!246)
Show authors on website (!245)
Add link to developer documentation in
CONTRIBUTING.rst
(!244)Remove Python 2.x leftover of specific
super()
call (!243)Use Gitlab for showing coverage and unit test reports (!241)
Use
black
formatter and 88 chars/line for the code and rst files (!240)Add return values for correlation analysis to all base classes (!235)
Added more linting for rst files (!239)
Bump minimum version of
tqdm
to 4.60 (!238)Add prompt toggle to examples (!236)
Added description to the ideal chemical potential how-to (!232)
Added quotation marks to command in tox.ini to account for spaces in paths (!232)
Fixed some typos and made minor modifications to the documentation (!232)
Cleanup .gitignore (!233)
More consistent molecule wrapping (!230)
Added missing AnalysisBase parameters to modules (!231)
created dark and light images and logo (!229)
Add explicit stacklevel arguments to warnings in the library (!236)
Switch to the build module (!234)
v0.7.2 (2023/01/09)¶
Philip Loche, Henrik Stooß
Remove superfluous group wise wrapping (!225)
Clarify unclear definition in Dieletric modules that could lead to wrong results (!228)
Fixed windows string manipulation in test CI (!227)
Added coverage posting on GitLab (!226)
Corrected wrong comparison in correlation analysis and added tests
Fixed link to changelog in pyproject.toml
Migrated versioneer to pyproject.toml
Added Support for Python 3.11
v0.7.1 (2023/01/01)¶
Henrik Stooß
Fix upload to PyPi. This release is identical to v0.7.
v0.7 (2022/12/27)¶
Philip Loche, Simon Gravelle, Marc Sauter, Henrik Stooß, Kira Fischer, Alexander Schlaich, Philipp Staerk
Make sure citation are only printed once (!260)
Added MacOS pipeline, fixed wheels (!218)
Fix CHANGELOG testing (!220)
Added dielectric how-to (!208)
Raise an error if
unwrap=False
andrefgroup != None
in dielectric modules (!215).Fix velocity profiles (!211)
Added the Theory to the Dielectric docs (!201)
Add a logger info for citations (!205)
Rename Diporder to DiporderPlanar (!202)
Change default behavior of DielectricPlanar: assume slab geometry by default (removing the
xy
flag and instead introduceis_3d
for 3d-periodic systems) (!202)Rename
profile_mean
toprofile
(!202)Major improvements on the documentation (!202)
Add a check if the CHANGELOG.rst has been updated (!198)
Fix behaviour of refgroup (!192)
Resolve +1 is summed for epsilon for each atom group (#101, !193)
Flatten file structure of analysis modules (#46, !196)
Consistent mass unit in docs
Porting examples to sphinx-gallery (!190)
Add
jitter
parameter to AnalysisBase (!183)Test output messages (!191)
Fixed typo in
DielectricPlanar
docs (!194)Add Sphere modules (!175)
Add
ProfileBase
class (!180)Slight restructure of the documenation (!189)
Fix py311 windows
Update build requirements for py310 and py311
Merged setup.cfg into pyproject.toml (!187)
Use versioneer for version info (!150)
Update project urls (!185)
Added repository link in the documentation (!184)
Added windows CI/CD pipeline (!182)
Update package discovery methods in setup.cfg
Refactor CI script (!181)
Fix
DielectricCylinder
(!165)Unified
n_bins
logging (#93, !179)Add MAICoS UML Class Diagramm (!178)
Changed density calculation using range in np.histogram (!77)
Update branching model in the documentation (!177)
remove ./ from index.rst
Improve documentation (!174)
Added reference for SAXS calculations (!176)
Update type of bin_pos in docs
Added
VelocityCylinder
moduleChange behavior of
sort_atomgroup
(#88, !152)get_compound
: option for returning indices of topology attributesAdded Tutorial for non-spatial analysis module (!170)
Check atomgroups if they contain any atoms (!172)
New core attributes:
bin_edges
,bin_area
,bin_volume
,bin_pos
&bin_width
(!167)Use
frame
dict instructure.py
(!169)Fix box dimensions for cylindrical boundaries (!168)
rmax
for cylindrical systems now uses correct dimensionsTransport module documentation update (!164)
Rename frame dict (!166)
Implement
SphereBase
andProfileSphereBase
(!162)Relative path for data (!163)
Create Linux wheels (!160)
Fix
Diporder
tests (!161)norm=number
: Declare bins with no atoms asnan
(!157)Simplify weight functions (!158)
v0.6.1 (2022/09/26)¶
Henrik Stooß
Fix the output of the ChemicalPotentialPlanar module (!173)
v0.6 (2022/09/01)¶
Philip Loche, Simon Gravelle, Srihas Velpuri, Henrik Stooß, Alexander Schlaich, Maximilian Becker, Kira Fischer
Write total epsilon as defined in paper (!155)
Introduce generic header (!149)
Fix error estimate in
EpsilonPlanar
(!153)Fix sym option in
EpsilonPlanar
(!148)Use standard error of the mean instead of variance for error estimate (!147)
Make all tests that write file use temporary file directory (!151)
Rewrite
Velocity
module usingProfilePlanarBase
(!142)Add
RDFPlanar
(!133)Refactor
EpsilonPlanar
(!139)Add a correlation time estimator (!137)
Add
frame
dict toAnalysisBase
(!138)Generalize
comgroup
attribute to all dimensions (!132)Output headers do not require residue names anymore (!134)
Remove
Debyer
class (!130)Generalize
concfreq
attribute inAnalysisBase
(!122)Fix broken binning in
EpsilonPlanar
(!125)Removed
repairMolecules
(!119)Added
grouping
andbin_method
option (!117)Bump minimum MDAnalysis version to 2.2.0 (!117)
Bump minimum Python version to 3.8 (!117)
Use base units exclusively (!115)
Higher tolerance for non-neutral systems (1E-4 instead of 1E-5)
charge``neutral decorator uses ``check_compound
nowAdd option to symmetrize profiles using
ProfilePlanarBase
(!116)Fix
comgroup
parameter working only in the z direction (!116)Remove
center
option fromProfileBase
(!116)Introduces new
ProfilePlanarBase
(!111)Split new
DensityPlanar
intoChemicalPotentialPlanar
,DensityPlanar
,TemperaturePlanar
(!111)Convert more
print
statements into logger calls (!111)Fix wrong
Diporder
normalization + tests (!111)Add
zmin
andzmax
to DensityPlanar and Diporder (!109)Fix EpsilonPlanar (!108)
More tests for
DensityPlanar
,DensityCylinder
,KineticEnergy
andDipoleAngle
(!104)Remove
EpsilonBulk
(!107)Add Code of Conduct (!97)
Fix lint errors (!95)
v0.5.1 (2022/02/21)¶
Henrik Stooß
Fix pypi installation (!98)
v0.5 (2022/02/17)¶
Philip Loche, Srihas Velpuri, Simon Gravelle
Convert Tutorials into notebooks (!93)
New docs design (!93)
Build gitlab docs only on master branch (!94, #62)
Removed oxygen binning from diporder (!85)
Improved CI including tests for building and linting
Create a consistent value of
zmax
in every frame (!79)Corrected README for pypi (!83)
Use Results class for attributes and improved docs (!81)
Bump minimum Python version to 3.7 (!80)
Remove spaghetti code in
__main__.py
and introducemdacli
as cli server library. (!80)Remove
SingleGroupAnalysisBase
andMultiGroupAnalysisBase
classes in favour of a unifiedAnalysisBase
class (!80)Change
planar_base
decorator to aPlanarBase
class (!80)Rename modules to be consistent with PEP8 (
density_planar
->DensityPlanar
) (!80)Use Numpy’s docstyle for doc formatting (!80)
Use Python’s powerful logger library instead of bare
print
(!80)Use Python 3.6 string formatting (!80)
Remove
_calculate_results
methods. This method is covered by the_conclude
method. (!80)Make results saving a public function (save) (!80)
Added docstring Decorator for
PlanarDocstring
andverbose
option (!80)Use
MDAnalysis
’s’center_of_mass
function for center of mass shifting (!80)
v0.4.1 (2021/12/17)¶
Philip Loche
Fixed double counting of the box length in diporder (#58, !76)
v0.4 (2021/12/13)¶
Philip Loche, Simon Gravelle, Philipp Staerk, Henrik Stooß, Srihas Velpuri, Maximilian Becker
Restructure docs and build docs for develop and release version
Include README files into sphinx doc
Add tutorial for density_cylinder module
Add
planar_base
decorator unifying the syntax for planar analysis modules asdenisty_planar
,epsilon_planar
anddiporder
(!48)Corrected time_series module and created a test for it
Added support for Python 3.9
Created sphinx documentation
Raise error if end is to small (#40)
Add sorting of atom groups into molecules, enabling import of LAMMPS data
Corrected plot format selection in
dielectric_spectrum
(!66)Fixed box dimension not set properly (!64)
Add docs for timeseries modulees (!72)
Fixed diporder does not compute the right quantities (#55, !75)
Added support of calculating the chemical potentials for multiple atomgroups.
Changed the codes behaviour of calculating the chemical potential if atomgroups contain multiple residues.
v0.3 (2020/03/03)¶
Philip Loche, Amanuel Wolde-Kidan
Fixed errors occurring from changes in MDAnalysis
Increased minimal requirements
Use new ProgressBar from MDAnalysis
Increased total_charge to account for numerical inaccuracy
v0.2 (2020/04/03)¶
Philip Loche
Added custom module
Less noisy DeprecationWarning
Fixed wrong center of mass velocity in velocity module
Fixed documentation in diporder for P0
Fixed debug if error in parsing
Added checks for charge neutrality in dielectric analysis
Added test files for an air-water trajectory and the diporder module
Performance tweaks and tests for sfactor
Check for molecular information in modules
v0.1 (2019/10/30)¶
Philip Loche
first release out of the lab