Changelog

v0.9 (2025/02/19)

Philip Loche, Marc Sauter, Kira Fischer, Federico Grasselli, Henrik Stooß, Adyant Agrawal

• Rewrite integrals in DielectricCylinder and DielectricSphere 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 is True and refgroup is not None (!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 and run method is the same as MDAnalysis.analysis.base.AnalysisBase (!297)

• Add frames and progressbar_kwargs argument to maicos.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 into str when using in sys.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 to build-macos (!283)

• Remove deprecated pytest tmpdir fixture (!283)

• Remove deprecated assert_almost_equal in favor of assert_allclose (!283)

• Move from os.path to pathlib.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) in maicos.Saxs to 0.1. (!279)

• Move cutils to cmath (!279)

• Add weight argument to maicos.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 of vac=True and is_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 and refgroup != 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 introduce is_3d for 3d-periodic systems) (!202)

• Rename profile_mean to profile (!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 module

• Change behavior of sort_atomgroup (#88, !152)

• get_compound: option for returning indices of topology attributes

• Added 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 in structure.py (!169)

• Fix box dimensions for cylindrical boundaries (!168)

• rmax for cylindrical systems now uses correct dimensions

• Transport module documentation update (!164)

• Rename frame dict (!166)

• Implement SphereBase and ProfileSphereBase (!162)

• Relative path for data (!163)

• Create Linux wheels (!160)

• Fix Diporder tests (!161)

• norm=number: Declare bins with no atoms as nan (!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 using ProfilePlanarBase (!142)

• Add RDFPlanar (!133)

• Refactor EpsilonPlanar (!139)

• Add a correlation time estimator (!137)

• Add frame dict to AnalysisBase (!138)

• Generalize comgroup attribute to all dimensions (!132)

• Output headers do not require residue names anymore (!134)

• Remove Debyer class (!130)

• Generalize concfreq attribute in AnalysisBase (!122)

• Fix broken binning in EpsilonPlanar (!125)

• Removed repairMolecules (!119)

• Added grouping and bin_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 now

• Add option to symmetrize profiles using ProfilePlanarBase (!116)

• Fix comgroup parameter working only in the z direction (!116)

• Remove center option from ProfileBase (!116)

• Introduces new ProfilePlanarBase (!111)

• Split new DensityPlanar into ChemicalPotentialPlanar, DensityPlanar, TemperaturePlanar (!111)

• Convert more print statements into logger calls (!111)

• Fix wrong Diporder normalization + tests (!111)

• Add zmin and zmax to DensityPlanar and Diporder (!109)

• Fix EpsilonPlanar (!108)

• More tests for DensityPlanar, DensityCylinder, KineticEnergy and DipoleAngle (!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 introduce mdacli as cli server library. (!80)

• Remove SingleGroupAnalysisBase and MultiGroupAnalysisBase classes in favour of a unified AnalysisBase class (!80)

• Change planar_base decorator to a PlanarBase 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 and verbose 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 as denisty_planar, epsilon_planar and diporder (!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