465b/nemf issues and pull requests

#95 - Change print statement when loading model

Issue - State: closed - Opened by 465b over 3 years ago
Labels: polish

#94 - get rid of the X,idx_A,idx_B of the doc of interaction functions?

Issue - State: open - Opened by 465b over 3 years ago
Labels: documentation, polish

#93 - doc of nutrient limited growth is wrong

Issue - State: closed - Opened by 465b over 3 years ago
Labels: bug, documentation, minor

#92 - alternative time scales for plots

Issue - State: open - Opened by 465b over 3 years ago
Labels: feature request

#91 - Add dependancy on environmental in interactions

Issue - State: open - Opened by 465b over 3 years ago
Labels: feature request

#90 - rename holling_type_0_inverse

Issue - State: open - Opened by 465b over 3 years ago - 1 comment
Labels: polish

#89 - load_model() is wront in doc example

Issue - State: closed - Opened by 465b over 3 years ago - 1 comment
Labels: bug

#88 - Add the option to enforce non-negativity for compartments

Issue - State: open - Opened by 465b about 4 years ago
Labels: feature request, major

#87 - Add option to pass kwargs to forward_model()

Issue - State: open - Opened by 465b about 4 years ago
Labels: feature request

#86 - Empty compartments become "recreated" even tho interactions wouldn't allow that

Issue - State: open - Opened by 465b about 4 years ago
Labels: bug, minor

#85 - Multi source interaction

Issue - State: open - Opened by 465b about 4 years ago
Labels: feature request

#84 - bug: wrong error message if verbose = False

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, minor

#83 - doc: inconsistencies

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: documentation

#82 - doc: add excel (xlmx) example

Issue - State: open - Opened by 465b over 4 years ago
Labels: documentation

#81 - YAML overhaul

Issue - State: open - Opened by 465b over 4 years ago
Labels: polish

#80 - Bounds of Interaction parameters are parsed as a set instead of a list

Issue - State: closed - Opened by 465b over 4 years ago
Labels: bug, minor

#79 - DOC: Talk about time steps in seconds

Issue - State: open - Opened by 465b over 4 years ago
Labels: documentation

#78 - bad method of importing with keys

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, minor

#77 - add load_reference_data() to api doc

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation

#76 - In load_model(), ref_data_path parameter not optional

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#75 - wrong key in load_reference_data when imported from yaml

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#74 - Check discrepency between the fitting quality

Issue - State: open - Opened by 465b over 4 years ago
Labels: bug

#73 - faulty docstring in holling III

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation

#72 - Parameters not plottet properly

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, minor

#71 - Write error message for - IndexError: If fitting parameters are compartments

Issue - State: open - Opened by 465b over 4 years ago - 1 comment
Labels: feature request, minor

#70 - negative ODE's

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, major

#69 - fix timestamp in excel input

Issue - State: closed - Opened by 465b over 4 years ago
Labels: bug, minor

#68 - yaml compartment parsing is inconsistent.

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: polish

#67 - make example accessible for user in python

Issue - State: open - Opened by 465b over 4 years ago
Labels: documentation, feature request

#66 - make example work in packaged version

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, feature request

#65 - switch away from "yaml" to either PyYAML or pyaml

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#64 - write parser to for csv refdata: datetime -> seconds

Issue - State: open - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#63 - "update_system_with_parameters" only correctly updates compartments

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#62 - automatize the construction of the "constraints" object for coupled optimization

Issue - State: open - Opened by 465b over 4 years ago
Labels: feature request, major

#61 - ReadTheDocs-Sphinx integration seems broken

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, documentation

#60 - Add a method to export/save data from the framework

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#59 - add t_eval to model.config['t_eval']?

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: design choice

#58 - adjust interaction graph to new sign'less interactions

Issue - State: closed - Opened by 465b over 4 years ago
Labels: bug

#57 - add time column with posix for time integration log data

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#56 - add option to log optimizer and time integration data seperatly

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#55 - re-add steady-state solution finder for scipy integration

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#54 - add data unification scripts

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#53 - add import ref_data function to model class

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#52 - user defined functions do not appear to be part of globals() or locals()

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#51 - add sphinx & readthedocs documentation for a more detailed documentation

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation

#50 - Add interaction plot call to README example

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation

#49 - Rename model_class() function to something like import_model()

Issue - State: closed - Opened by 465b over 4 years ago
Labels: polish

#48 - Rename interaction functions variables to be more verbose

Issue - State: open - Opened by 465b over 4 years ago
Labels: polish

#47 - Add install notes for windows users

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation

#46 - shall the framework be usable from the command line?

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: design choice

#45 - integrate more sophisticated, third party IVP(ODE)-solver

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request, design choice

#44 - integrate more sophisticated, third party non-linear programming solvers

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request, design choice

#43 - add documentation for debugging the typical problems

Issue - State: open - Opened by 465b over 4 years ago
Labels: documentation

#42 - shall "optimisation" flag in yaml be optional?

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: design choice

#41 - add sanity check for: shape(reference data)==shape(defined optimisations)

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments
Labels: feature request

#40 - redirect automated data output

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, feature request, design choice

#39 - add documentation for writing and using interaction functions

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: documentation, feature request

#38 - add a directed loop representatin to the graph plot

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#37 - add dependencies to module package

Issue - State: closed - Opened by 465b over 4 years ago

#36 - add comments to exemplary configuration files

Issue - State: closed - Opened by 465b over 4 years ago

#35 - test and potentially remove the soft barrier enforcement

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments
Labels: bug, feature request, design choice

#34 - package library

Issue - State: closed - Opened by 465b over 4 years ago

#33 - restructure user-faced functions

Issue - State: closed - Opened by 465b over 4 years ago

#32 - Add sensitivity analysis?

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#31 - add feature to fit non-steady-state solutions

Issue - State: closed - Opened by 465b over 4 years ago - 3 comments
Labels: feature request

#30 - Update documentation

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug, feature request

#29 - The functionality of sources and sinks got lost

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#28 - Potential bug if interaction function does not require parameters

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: bug

#27 - add sanity checks to test to the model_config input

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment

#26 - make network plot configuration dump pretty

Issue - State: closed - Opened by 465b over 4 years ago

#25 - remove the hardcoding of the interaction model

Issue - State: closed - Opened by 465b over 4 years ago
Labels: bug

#24 - Bug in parameter selection during the optimisation

Issue - State: closed - Opened by 465b over 4 years ago
Labels: bug

#23 - add decent default output plotting

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#22 - make it possible to optimise coupled function parameters

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments
Labels: feature request

#21 - add verbose option at runtime

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#20 - write unit tests

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#19 - write yaml documentation

Issue - State: closed - Opened by 465b over 4 years ago
Labels: documentation, feature request

#18 - remove compartments from yaml config

Issue - State: closed - Opened by 465b over 4 years ago
Labels: feature request

#17 - gradient descent calculates "center " prediction/cost twice

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#16 - use of model_configuration in function is inconsistant

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments
Labels: feature request

#15 - rewrite run_time_evo to be "model_configuration" independant

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#14 - add a visualisation tool of the interaction graph

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment
Labels: feature request

#13 - rewrite/design gradient_descent such that it only takes the position on the costfunction as input

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments
Labels: feature request

#12 - sanity check algorithm for flows

Issue - State: closed - Opened by 465b over 4 years ago - 2 comments

#11 - add a function to contain the 'differential operator'

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment

#10 - add a method that checks if everything has a flow into a detritus compartment

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment

#9 - column normalisation in the coefficient matrix does not consider set constrains

Issue - State: closed - Opened by 465b over 4 years ago - 1 comment

#8 - stability checks fails or is imprecise if absolute value is close to zero

Issue - State: closed - Opened by 465b almost 5 years ago - 1 comment
Labels: bug

#7 - iteration step counter in barrier_hard_enforcement() is wrongly implemented

Issue - State: closed - Opened by 465b almost 5 years ago - 1 comment
Labels: bug

#6 - some object share the same name, even though they differ in dimension

Issue - State: closed - Opened by 465b almost 5 years ago - 2 comments
Labels: feature request

#5 - add 'natural' stop in optimization if sufficiently converged

Issue - State: closed - Opened by 465b almost 5 years ago
Labels: feature request

#4 - Create LICENSE

Pull Request - State: closed - Opened by 465b almost 5 years ago

#3 - barrier_function returns "inf" if on boarder - breaks gradient method

Issue - State: closed - Opened by 465b about 5 years ago
Labels: bug

#2 - add feature that enforces positive masses

Issue - State: closed - Opened by 465b about 5 years ago - 1 comment
Labels: feature request

#1 - unify integration schemes and time evolution schemes

Issue - State: closed - Opened by 465b about 5 years ago - 1 comment
Labels: feature request

GitHub / 465b/nemf issues and pull requests