Releases: mazzalab/pyntacle
Releases · mazzalab/pyntacle
Pyntacle v.1.3.1
Bug fixes:
#47 -nprocs removed in keyplayer kp-info command line
#48 empty result with kp-finder
#49 -seed argument removed in pyntacle generator
#50 --plot-format option removed from 1.2 onward
#51 seed argument removed in group degree API
#52 bad handling of missing output file names
#53 bad handling of empty set due to graph intersection
Pyntacle v.1.3
Major updates:
- [algorithms] Implementation of the new Stochastic Gradient Descent (SGD) search algorithm (#31)
- [tests] Tests for SGD included (#35)
- [environment] Upgraded base Python version to 3.7 (#34)
- [environment] Install igraph ver. 0.8.2 (conda-forge) (#41)
Minor updates:
- removed dependency to Cairo and the old plotter (#32)
Pyntacle v.1.2
Major updates:
- [command-line] The algorithm that decides the computing configuration to be used to analyze a give graph was updated to exclude the possibility to run multi-process and multi-threaded at the same time. This is still possible accessing directly to the APIs.
- [command-line] Renamed option from -T/--threads to -O/--nprocs to avoid clashes with other synonymous options
- [API] Removed all decorator methods that over-checked the sanity of the arguments of methods. These resulted to improve.
- [PyntacleInk] bug #28 "initial value" and "value" are swapped, solved
- [Tests] bug #25 "gr-finder bruteforce test fails", solved
Minor:
- [command-line] bug #23 "the command line option --type m-reach in kp-finder produces no output", solved
- [API] removed the max_distance argument from all methods
- [API] removed the seed from each method. Postponed to later versions the implementation of a clever manner of controlling randomness of number generators
the default number of forked processes is now 1 and not equals to the total number of available processors -1
removed shortest_path_modifications.py file
Pyntacle v.1.1
- PyntacleInk released! A standalone and interactive html file is produced in place of a static pdf.
- Several bugfixes
Pyntacle v0.2.4
- fixed tests in order to accommodate changes in the output.
- reports now properly show the names of the metrics without underscores
- minor fixes in log shell of pyntacle metrics
- removed metavar from the '--suppress-cursor' option as it confilcted with the "store_true" option
- restored igraph as default sp implementation for bruteforce threading because of unresolved Numba conflicts
Pyntacle v0.2.3.3
- correct version numbering
- fixed some log messages
- changed the help for the
communitiescommand - removed spaces in summary report
- test for experimenting colorama on summary report
- fixed Pyntacle case for many commands, for a better clarity between the method name and the command line options
- brute-force search now reports all the sets in a separate line, making
the interpretation and readability clearer - greedy-optimization now reports the name of the set in a new line, making
the interpretation and readability clearer
Pyntacle v0.2.3.2
- fixed major bug addressing a numpy array object in greedyoptimization
- minor code cleaning
Pyntacle v0.2.3.1
- improved decision-making regarding implementation in add_attributes
- enabled multiprocessing in kp-finder, brute-force search
- moved the --threads option in kp-finder only.
- the edge attribute "node_names" was changed to "adjacent_nodes"
- renamed file handles in importer and exporter scripts for graph and attributes methods
- redirected output of importers and exporters to stdout instead of log
- general cleanup of stdout messages
Pyntacle v0.2.2
- fixed a refactoring bug in LocalTopology
Pyntacle v0.2.1
-
Fixed a bug in generate - small-world with the -R option: all the graphs (starting from the 2nd on) were identical. Replaced the built-in random with numpy.random
-
--plot-layout option added to all the commands that produce plots.
-
Minor corrections in the inline help.