0.6.0 changes: Plots, bugfixes (#44)

* slow_flow! bugfix to keep higher-order diffs

* remove deprecated code

* Plots implemented

* time-dependent plots

* progress bars stdout fix

* random_warmup made default

* LimitCycles module and docs

* LinearResponse cleanup

* plot defaults

* caps updated, version 0.6.0

* examples cleanup

* newton solving added

* docs plotting, time evo, lin resp

Author: jkosata

Project.toml

@@ -1,11 +1,10 @@
 name = "HarmonicBalance"
 uuid = "e13b9ff6-59c3-11ec-14b1-f3d2cc6c135e"
 authors = ["Jan Kosata <[email protected]>", "Javier del Pino <[email protected]>"]
-version = "0.5.2"
+version = "0.6.0"
 
 [deps]
 BijectiveHilbert = "91e7fc40-53cd-4118-bd19-d7fcd1de2a54"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
@@ -18,29 +17,25 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Peaks = "18e31ff7-3703-566c-8e60-38913d67486b"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 BijectiveHilbert = "0.3.0"
-Conda = "1.6.0"
 DSP = "0.7.4"
 DataStructures = "0.18.13"
-DifferentialEquations = "7.3.0"
+DifferentialEquations = "7.5.0"
 Distances = "0.10.7"
 DocStringExtensions = "0.8.6"
 FFTW = "1.5.0"
 HomotopyContinuation = "2.6.4"
-JLD2 = "0.4.22"
+JLD2 = "0.4.24"
 Latexify = "0.15.16"
 Peaks = "0.4.0"
+Plots = "1.35.0"
 ProgressMeter = "1.7.2"
-PyCall = "1.93.0"
-PyPlot = "2.10.0"
 Symbolics = "4.10.4"
 julia = "1.8.0"
 

README.md

@@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 HarmonicBalance = "e13b9ff6-59c3-11ec-14b1-f3d2cc6c135e"
 
 [compat]
-Documenter = "0.27.12"
+Documenter = "0.27.23"

docs/Project.toml

@@ -12,12 +12,10 @@ makedocs(
 			"background/stability_response.md"
 		],
 		"Examples" => Any[
-			"examples/single_Duffing.md"
+			"examples/simple_Duffing.md"
 			"examples/linear_response.md"
 			"examples/time_dependent.md"
-			"examples/single_parametron_1D.md"
-			"examples/single_parametron_2D.md"
-			"examples/single_parametron_time_dep.md"
+			"examples/parametron.md"
 			],
 		"Manual" => Any[
 			"manual/entering_eom.md"