Circuitscape.jl

Circuitscape v5.8.0

Diff since v5.7.1

Closed issues:

• disable logging during tests (#222)
• Fix or remove codecov badge (#250)
• effective resistance for one-to-all (#252)
• Denied access to folder (#261)
• Pkg.test("Circuitscape") fail on new installation (#266)
• trouble with variable source strengths (#268)
• "Error: syntax: invalid escape sequence" (#271)
• ValueError: could not broadcast input array fro, shape (3,1) into shape (3) (#272)
• ERROR: KeyError: key "Zlib_jll" not found (#274)
• Move CI/docs building to GitHub Actions (#275)
• BoundsError (#287)
• Tests fail with ArchGDAL 0.6.0 (#290)

Merged pull requests:

• Add option to use MKL Pardiso, reduce number of tests (#225) (@ranjanan)
• Use ArchGDAL.write() to persist rasters to disk. (#263) (@yeesian)
• Use do-blocks for managing rasters via ArchGDAL (#264) (@yeesian)
• Move documentation to Documenter (#265) (@ranjanan)
• Disable logging during tests (#267) (@ranjanan)
• Rework alltoone mode with and without var strengths (#270) (@ranjanan)
• CompatHelper: bump compat for "IterativeSolvers" to "0.9" (#279) (@github-actions[bot])
• CompatHelper: bump compat for "AlgebraicMultigrid" to "0.4" (#280) (@github-actions[bot])
• Fix ASCII header in some test files (#291) (@vlandau)
• tol -> reltol (#293) (@ranjanan)
• CompatHelper: add new compat entry for "AlgebraicMultigrid" at version "0.4" (#294) (@github-actions[bot])

Circuitscape v5.7.1

Diff since v5.7.0

Closed issues:

• InexactError: Int64 (#257)
• Add warning when there are non-integers in node file (#258)
• Error when using Circuitscape from R (#262)

Merged pull requests:

• add informative error throw if node file (point_file) contains non-integers (#259) (@vlandau)

Circuitscape v5.7.0

Diff since v5.6.0

Closed issues:

• julia version and Circuitscape (#251)
• Installing master branch of Circuitscape fails (#254)

Merged pull requests:

• add option to suppress @info (#255) (@vlandau)

Circuitscape v5.6.0

Diff since v5.5.5

Closed issues:

• New CHOLMOD memory errors (#150)
• Pkg.test("Circuitscape"): Single test failure - Raster Pairwise (#178)
• Make 64-bit indexing default. Was ERROR: LoadError: InexactError: trunc(Int32, 2147483653) (#200)
• ERROR: BoundsError: attempt to access 0-element Array{SharedArrays.SharedArray{Float64,2},1} at index [1] (#201)
• Failing tests in Raster one to all in Julia 1.4-dev (#202)
• JSExpr: Unsupported string expression, "$(e)"JSExpr: Unsupported string expression, "$(e)" 64-bit Windows installer (#208)
• Bounds error (#209)
• Error: zero resistance values are not currently supported for habitat maps. Use a shor circuit region file instead (#210)
• ERROR: LinearAlgebra.LAPACKException(2) (#211)
• Test failure on mac due to too many open shm segments (#212)
• Experiment with METIS ordering in cholesky (#213)
• Trouble executing script with specified library location (#214)
• Please reopen if the issue persists. (#215)
• No output with completed script (#216)
• Experiment with PARDISO solvers from MKL (#218)
• Add possibility to save as .tif with compression (#220)
• New GUI using Gtk? (#228)
• Circuitscape in Julia unable to process a 1.4 Billion pixel landscape (#232)
• GZip requirement 0.5.1 can't be met (#234)
• Maximum amount of pairs and batch processing (#235)
• InexactError while parsing nodata values (#239)
• More issues with opened files on Mac (#241)
• ArchGDAL version dependency error (#244)
• write_as_tif options only works if value is true, not True (#246)

Merged pull requests:

• Make 64 bit indexing default (#206) (@ranjanan)
• Fix a bug where max curr was not being initialized properly (#207) (@ranjanan)
• Install TagBot as a GitHub Action (#219) (@JuliaTagBot)
• Vl/travis - dependency stuff (#221) (@vlandau)
• Add a few closes for filehandles. (#223) (@ViralBShah)
• add tif/asc read and write support (#229) (@vlandau)
• Pkg.checkout not supported anymore (#237) (@VLucet)
• Fix InexactError in Read Raster (#240) (@vlandau)
• Modify default call to pmap when paralellizing (#243) (@VLucet)
• Check for write_as_tif to be in TRUELIST (#247) (@VLucet)

v5.5.5 (2019-11-29)

Diff since v5.5.4

Closed issues:

• GZip broken for Windows in Julia 1.3, so Circuitscape (and Omniscape) also broken (#203)
• ERROR: Failed to read habitat map. There may be errors in your file. (#198)
• Error : UndefVarError : warn not defined (#193)
• Two Issues: Memory Error and Not working on my desktop (#191)
• Very Slow Processing (#190)
• Potential speedups (#174)

Merged pull requests:

• update GZip version in MANIFEST (#205) (vlandau)
• updated GZip dep (#204) (vlandau)
• Some bug squashing for INIBuilder (#195) (ranjanan)
• Add new UI (#194) (ranjanan)

v5.5.4 (2019-08-06)

Diff since v5.5.3

Closed issues:

• Documentation Clarification (#186)
• Questions from your “average user” (#179)
• how to cite circuitscape.jl? (#173)
• Warn() deprecated (#171)

• Parallelism in one to all and all to one modes
• Fix long standing include pairs bugs

• Upgrades to Memento v0.7.0
• Stabilises the solver with some simple regularisation
• Fix a performance bug in advanced mode that stalls voltages being assigned to cells
• Fix a bug in shortcut mode while using the CHOLMOD solver which makes it do extra work
• Introduce a flag that lets you bump indexing to Int64

Bug fix for:

• not entering shortcut mode when we want cumulative maps and no other voltage or current maps

Includes the following fixes:

1. Parallel cumulative maps for raster mode (#123)
2. Batch mode for CHOLMOD (#126)

Fixes the following bugs:

• Improves logging for shortcut calculation mode (#109)
• Adds 1 as a way of specifying true (#112)
• Improves logging for when point files have polygons (#117)
• Fixes the 3 column resistance file bug (#120)
• Adds utils for reading and writing cum and max current maps (#115)