Circuitscape.jl

Circuitscape v5.13.3

Diff since v5.13.2

Merged pull requests:

• Increase error tolerance for advanced mode (#410) (@vlandau)

Circuitscape v5.13.2

Diff since v5.13.1

Merged pull requests:

• Bump actions/checkout from 3 to 4 (#395) (@dependabot[bot])
• CompatHelper: bump compat for AlgebraicMultigrid to 0.6, (keep existing compat) (#396) (@github-actions[bot])
• Bump actions/cache from 3 to 4 (#404) (@dependabot[bot])
• increase solve error tolerance from 1e-6 to 1e-4 (#407) (@vlandau)
• Bump codecov/codecov-action from 3 to 4 (#409) (@dependabot[bot])

Closed issues:

• pkg test failed (#364)
• Precompilation warning for a missing type (#403)
• Increase tolerance of assert check for solve accuracy, or add option to allow failure. (#406)

Circuitscape v5.13.1

Diff since v5.13.0

Closed issues:

• "KeyError: key ([#],[#]) not found" (#260)
• Julia states my habitat file is empty (#366)
• Circuitscape stop working in advanced and one-to-all mode (#382)

Merged pull requests:

• CompatHelper: add new compat entry for DelimitedFiles at version 1, (keep existing compat) (#391) (@github-actions[bot])
• CompatHelper: bump compat for GZip to 0.6, (keep existing compat) (#392) (@github-actions[bot])
• In advanced mode, write current maps if any of the current map flags are true (#393) (@ranjanan)
• Release 5.13.1 (#394) (@ranjanan)

Circuitscape v5.13.0

Diff since v5.12.3

Merged pull requests:

• Update Julia version compat to 1.9 (#384) (@ranjanan)

Circuitscape v5.12.3

Diff since v5.12.2

Merged pull requests:

• Fix indexing while reading source and ground files (#378) (@ranjanan)

Circuitscape v5.12.2

Diff since v5.12.1

Closed issues:

• .out file not correct (#159)
• ERROR: DimensionMismatch (#199)
• Include pairs not implemented in the polygon focal point case (#278)
• ncol warning (#285)
• Included pairs file ignored (#341)
• Short circuit regions not recognized (#353)
• Assertion error: linear solve did not converge in single precision (#362)
• Nothing happens after first round of calculations in all-to-one mode (#367)
• AssertionError: norm(G * v .- curr) / norm(curr) - multiple failures (#370)

Merged pull requests:

• add include pairs logic when polygons in point files (#374) (@ranjanan)
• write correct solver in output file (#375) (@ranjanan)
• network: check if nodes start from zero (#376) (@ranjanan)

Circuitscape v5.12.1

Diff since v5.12.0

Closed issues:

• Error happens in Julia. "At least one focal node location falls outside of habitat map" (#360)
• Invalid index Error, but model runs fine on GUI (#368)
• Advanced run not completing (see also #131) (#369)

Merged pull requests:

• While making current maps, check for both (node1,node2) and (node2,node1) (#372) (@ranjanan)
• Speedup a common advanced mode calc (#373) (@ranjanan)

Circuitscape v5.12.0

Diff since v5.11.2

Closed issues:

• ERROR: LoadError: InitError: could not load library "libproj.so" libcurl.so: version `CURL_4' not found (#352)
• Error issue question (#356)

Merged pull requests:

• CompatHelper: bump compat for ArchGDAL to 0.9, (keep existing compat) (#361) (@github-actions[bot])
• Move Pardiso solver to lib (#371) (@ranjanan)

Circuitscape v5.11.2

Diff since v5.11.1

Closed issues:

• ERROR: ArgumentError: column indices J[k] must satisfy 1 <= J[k] <= n (#333)
• ArgumentError: dense matrix construction failed for unknown reasons (#334)

Merged pull requests:

• fix sparse mat constrcution (#357) (@ranjanan)

Circuitscape v5.11.1

Diff since v5.11.0

Closed issues:

• AssertionError: norm(G * v .- curr, Inf) / norm(v, Inf) < 1.0e-5 (#345)
• Core Mapper not reading .xlsx file (#347)
• ERROR: SuiteSparse.CHOLMOD.CHOLMODException("") (#351)

Merged pull requests:

• Make assertion check consistent with iterativesolvers.jl (#348) (@ranjanan)

Circuitscape v5.11.0

Diff since v5.10.2

Merged pull requests:

• CompatHelper: bump compat for AlgebraicMultigrid to 0.5, (keep existing compat) (#343) (@github-actions[bot])
• Bump deps versions. Disable Pardiso tests (#346) (@ViralBShah)

Circuitscape v5.10.2

Diff since v5.10.1

Closed issues:

• Ground files need to take in txt files (advanced mode) (#338)

Merged pull requests:

• Some txt file reading logic for advanced mode (#339) (@ranjanan)

Circuitscape v5.10.1

Diff since v5.10.0

Closed issues:

• Install Error due to GDAL: libgdal-28.dll module could not be found (#329)
• CS tries to solve thousands of pairs (#332)

Circuitscape v5.10.0

Diff since v5.9.1

Closed issues:

• Issue branch_current output in network mode (#282)
• memory error (#292)
• ERROR: MethodError: no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int64,Float64}) (#325)
• Empty output file (#327)
• Current file not written? Circuitscape runs, but has no output (#328)

Merged pull requests:

• Fix some cumulative current map logic (#330) (@ranjanan)

Circuitscape v5.9.1

Diff since v5.9.0

Merged pull requests:

• Add internal function to use in Omniscape (#326) (@vlandau)

Circuitscape v5.9.0

Diff since v5.8.4

Closed issues:

• Create cumulative branch and node currents in network mode (#119)
• ERROR: ArgumentError: column indices J[k] must satisfy 1<= J[k] <= n (#281)
• Error with networks consisting of multiple components (#283)
• Circuitscape 5 is not writing cumulative branch and node current files for network mode (#303)
• ERROR: SuiteSparse.CHOLMOD.CHOLMODException("") (#316)
• Test failed on Debian : no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int64, Float64}) (#321)

Merged pull requests:

• Currents and cumulative currents in network mode (#318) (@ranjanan)
• Move to Graphs from LightGraphs (#319) (@ranjanan)
• Network advanced - connected components (#320) (@ranjanan)
• CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#322) (@github-actions[bot])
• CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#323) (@github-actions[bot])
• Add info about 0 vs 1 based indexing, throw error if not 0 or 1 (#324) (@ranjanan)

Circuitscape v5.8.4

Diff since v5.8.3

Closed issues:

• Compress grids has no effect (#168)
• Blank screen on GUI after running main executable (#192)
• Convert circuitscape manual to Julia Documenter format (#242)
• Get CI to pass (#245)
• Pemission denied and paralell processes number (#284)
• Docs point to non-existent "examples" folder for examples (#286)
• Cumulative current map all NODATA in circuitscape.jl, but show currents in circuitscape GUI (#289)
• CHOLMOD solver error (#300)
• AssertErrors for several users -- norm(G * v - curr) < 1e-6 check failing (#305)
• MethodError: no method matching Circuitscape.RasterData(::Matrix{Float64}, ::Matrix{Int64}, ::Matrix{Float64}, ::Matrix{Float64}, ::Tuple{Vector{Int64}, Vector{Int64}, Vector{Int64}}, ::Matrix{Float64}, ::Nothing, ::Circuitscape.RasterMeta) (#306)
• What wrong by "output/mgNetworkVerify1.out" (#307)
• Circuitscape 5.0.0 with INIBuilder: habitat_map_is_resistance = resistance incorrectly treats habitat map as conductance. (#312)
• GDALError (CE_Failure, code 1): write failed, disk full? (#314)
• resistance_3columns file (#315)

Merged pull requests:

• Add better error message when include pairs file is incorrect (#310) (@ranjanan)
• builder passed incorrect value to habitat_map_is_resistances, (#313) (@vlandau)
• remove references to examples directory from docs (#317) (@vlandau)

Circuitscape v5.8.3

Diff since v5.8.2

Closed issues:

• Pkg.test("Circuitscape") fail in double precision, raster pairwise and advanced (Ubuntu) (#302)

Merged pull requests:

• Ask for > 5 digits of precision when solving linear system (#309) (@ranjanan)

Circuitscape v5.8.2

Diff since v5.8.1

Closed issues:

• Make new release with AMG 0.4.0 (#276)
• AssertionError: norm(asolve * volt .- sources) < 1.0e-5 in "all-to-one" mode using the latest development version of Circuiscape. v5.7.1 (#288)

Merged pull requests:

• CompatHelper: bump compat for "ArchGDAL" to "0.7" (#301) (@github-actions[bot])
• Update Pardiso deps, julia deps (#304) (@ranjanan)
• Update issue templates (#308) (@ranjanan)

Circuitscape v5.8.1

Diff since v5.8.0

Closed issues:

• Cholmod for advanced mode (#136)

Merged pull requests:

• Pass the suppress_messages arg to some functions new to 5.8.0 (#296) (@vlandau)
• Reduce error tolerance for matrix norms when using single precision (#297) (@vlandau)
• Revert "Reduce error tolerance for matrix norms when using single pre… (#298) (@ranjanan)
• Redo of assert tolerance after accidental revert of previous PR (#299) (@vlandau)