1.7
- Implemented bug fixes following feedback from John J. Low.
- Introduced updated installation instructions with constrained package versions.
- Enhanced support for osx-arm64 architectures on the installation instructions following feedback from John J. Low.
- Fixed a bug introduced in connectivity logic in 1.6.
- Fixed some minor GUI bugs.
- New streamlined connectivity load/save logic implemented.
- Switched to f2_modified, which supports python>=3.9 and has implemented size-aware node repulsion.
- Implemented customizable node repulsion network layout calculations.
- The display of graph plots is now handled by pillow.
1.6
- New "Assume grid" connectivity prediction mode that significantly accelerates the neighboring calculations for homogeneously distributed datasets (the most common use case).
- Fixed subtle bug with global node ids annotation that could produce an error when selecting non-minimum origin or target points and could block network plots from working with networks containing disconnected regions.
- Added a check for the existence of disconnected regions that reports a warning message.
- Added a check for coordinate redundancy to prevent the use of artefactual surfaces.
- Thanks to Dr. Marcelo D. Polêto's feedback, an automatic data type reduction function to reduce memory usage was implemented.
- Thanks to Dr. Marcelo D. Polêto's feedback, the connectivity calculations were rewritten to reduce memory usage.
- Changed the way fragmentwise path is saved to avoid extensive memory use when extremely complex paths are calculated.
- Major overhaul of the "Energy profiles" and "Coordinate projections" point labeling logic. Now only minimum or barrier points are labeled, indicating the cluster number to which they belong.
- Made it possible to plot "Coordinate projections" without choosing any point.
- MEPSAnd no longer requires igraph, ForceAtlas2 or cairo to run. If any of these packages is not detected, "Network projections" will be disabled but everything else will work as usual.
- Replaced "dype=np.int" instances with "dtype=np.int_".
- Added terminal report messages indicating the number of neighbors found as a quick sanity check for connectivity calculations.
- Added terminal report messages indicating minima propagation progress.
- Removed instances of fig.gca(projection='3d') as it is deprecated matplotlib.
- Instances of "map_" in the source code have been replaced with "surface_" to unify terminology.
- Fixed well sampling calculations not identifying origin or target clusters correctly.
- Minor code cleaning.
- A "Good practices" section has been added to the manual, with a particular focus on metadynamics, based on Dr. Marcelo D. Polêto's reports.
1.5
- Withdrawn release.
1.41
- Added the correct citation reference to MEPSAnd.py, replacing the previous "XXXX..." placeholder.
- Updated the citation reference in the manual, as the paper is no longer "in press".
1.4
- Number formatting in "save_simplified_path_to_txt" method has been modified to improve the readability of the resulting files.
1.35
- BUGFIX: a bug introduced during network projection rewriting in 1.3 broke the ability to properly assign default plotting parameters in "barriers as vertices" graphs.
1.3
- Major fix: network projection edge selection was not working as intended and has been completely rewritten.
- Minor bugfixes to the GUI.
- Minor code cleaning.
1.2
- BUGFIX: As reported by Oriol Esquivias, the method to save minimum and barrier clusters was broken when clusters of more than one point were present. Fixed using an index array ("index_array") with the adequate shape in the "np.column_stack" calls of the "save_minbar_clusters_to_txt" method.
- Changed how the MEPSAnd version is printed on the terminal when it is launched to improve version readability.
1.1
- BUGFIX: As reported by Oriol Esquivias, instances of pandas compat.StringIO could lead to incompatibility issues with pandas 0.25.1. Thus, all instances of pd.compat.StringIO have been replaced with io.StringIO.
