Merge remote-tracking branch 'origin/master' into pja/externalize-cus…

…tom-generators

Project.toml

@@ -1,6 +1,6 @@
 name = "MatrixDepot"
 uuid = "b51810bb-c9f3-55da-ae3c-350fc1fbce05"
-version = "1.0.4"
+version = "1.0.5"
 
 [deps]
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
@@ -15,7 +15,7 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 CodecZlib = "0.6, 0.7"
-DataFrames = "0.20, 0.22, 0.21, 1.1"
+DataFrames = "0.20, 0.22, 0.21, 1.1, 1.2, 1.3"
 MAT = "0.7, 0.8, 0.9, 0.10"
 Scratch = "1"
 julia = "1"

README.md

@@ -84,14 +84,14 @@ start with a letter and contain only letters, digits, and `'_'`.
 
 Every matrix has a numeric identifier, which is unique for its area:
 
-  * `builtin(id)` - one of the built-in matrix generators - currently `id ∈ 1:59`.
-
-  * `user(id)` - a user-defined matrix generator - starting with `1`.
+* `builtin(id)` - one of the built-in matrix generators - currently `id ∈ 1:59`.
 
-  *  `sp(id)` - one of the `SuiteSparse` collection. The integer ids are the
+* `user(id)` - a user-defined matrix generator - starting with `1`.
+
+* `sp(id)` - one of the `SuiteSparse` collection. The integer ids are the
   'official' ident numbers assigned by the collection. Currently `id ∈ 1:3000`.
 
-  * `mm(id)` - one of the `MatrixMarket` collection. Here id follows the ordering
+* `mm(id)` - one of the `MatrixMarket` collection. Here id follows the ordering
   of the index file of the collection.
 
 ### Sets of Matrix Names - Pattern
@@ -105,7 +105,7 @@ The following pattern types are supported:
   1. `"name"` - a string matching exactly a matrix name
   2. `"shell-pattern"` - a string with shell wildcards `'?', '*', "[...]"` included.
 
-  3. `r"egular expression"` - a regular expression to match the matrix name. 
+  3. `r"egular expression"` - a regular expression to match the matrix name.
 
   4. `:group` - one of the defined group names; match all matrices in the group
 
@@ -131,10 +131,12 @@ The set of all known matrices can be expressed as empty tuple `()`. In a shell-
 pattern the double `**` matches also slash characters, in contrast to the single `*`.
 
 A convenient form of a predicate-generator is
+
 ```julia
 @pred(expression)
 ```
-where expression is a valid `Julia` boolean expression, which may access all 
+
+where expression is a valid `Julia` boolean expression, which may access all
 properties of `MatrixData` as literal variable names.
 
 Examples:
@@ -144,15 +146,15 @@ Examples:
 
 `@pred(500_000 <= n * m < 1_000_000)` restricts the size of matched matrices.
 
-`@pred(10^4 <= n <= 2*10^4 && n == m && nnz / n > 10 )` in average more than 10 entries per row 
+`@pred(10^4 <= n <= 2*10^4 && n == m && nnz / n > 10 )` in average more than 10 entries per row
 
 There is s set of predefined predicate functions including:
 `(issymmetric, ishermitian, isgeneral, isskew, isreal, iscomplex, isboolean,
 islocal, isremote, isloaded, isunloaded, isbuiltin, isuser, issparse)`
 
 Special predicate generators `keyword(word...)` and `hasdata(symbol...)` allow to
 support keyword-search and check for the existence of meta-data.
-For example: `hasdata(:x) & ~keyword("fluid")` provides solution (x) and does not mention "fluid". 
+For example: `hasdata(:x) & ~keyword("fluid"` provides solution (x) and does not mention "fluid".
 
 ## Accessing Data
 
@@ -185,34 +187,34 @@ mdinfo(pattern) # individual documentation about matrix(es) matching pattern
 
 In general the first form is preferrable, if only the pure matrix is required.
 For remote collections no arguments are used.
- 
+
 The second form allows to access all types of 'meta-data', which may be available for some local or remote matrices.
 
 Examples:
 
-`md = mdopen("spikes", 5, false); A = md.A; b = md.b; x = md.x`  
+`md = mdopen("spikes", 5, false); A = md.A; b = md.b; x = md.x`
 
 `md = mdopen("Rommes/bips07_1998"); A = md.A; v = md.iv; title = md.data.title;
  nodenames = md("nodename.txt")`
 
 The last example shows, how to access textual meta-data, when the name contains
-`Julia` non-word characters. Also if the metadata-name is stored in a variable, 
+`Julia` non-word characters. Also if the metadata-name is stored in a varaible,
 the last form has to be used.
 
 `meta = metasymbols(md)[2]; sec_matrix = md(meta)`
 
 The function `metasymbols` returns a list of all symbols denoting metadata
 provided by `md`. Wether expressed as symbols or strings does not matter.
 
-The system function `propertynames(md)` returns all data of `md`. That includes 
+The system function `propertynames(md)` returns all data of `md`. That includes
 size information and metadata.
 
 `propertynames(md.data)` gives an overview about all attributes of the
 `md.data::MatrixData`, which can for example be used in the `@pred` definitions.
 
 ### Backoffice Jobs
 
-The remote data are originally stored at the remote web-site of one of the 
+The remote data are originally stored at the remote web-site of one of the
 matrix collections. Before they are presented to the user, they are downloaded
 to local disk storage, which serves as a permanent cache.
 
@@ -276,7 +278,6 @@ Example:
 `MatrixDepot.load(sp(:) & @pred(nnz < 100_000))` to download only problems with given
 number of stored entries in the main matrix.
 
-
 ## Sample Session
 
 To see an overview of the matrices in the collection, type
@@ -288,7 +289,7 @@ julia> mdinfo()
   Currently loaded Matrices
   –––––––––––––––––––––––––––
 
-builtin(#)                                                                                                                
+builtin(#)
 –––––––––– ––––––––––– ––––––––––– ––––––––––– –––––––––– –––––––––––– ––––––––––– ––––––––––– ––––––––––––– ––––––––––––
 1 baart    7 circul    13 fiedler  19 gravity  25 invhilb 31 magic     37 parter   43 randcorr 49 shaw       55 ursell
 2 binomial 8 clement   14 forsythe 20 grcar    26 invol   32 minij     38 pascal   44 rando    50 smallworld 56 vand
@@ -301,15 +302,15 @@ user(#)
 –––––––––
 1 randsym
 
-Groups                                                                                      
+Groups
 –––––– ––––––– ––––– –––– ––––– ––––– ––––––– ––––––– –––––– –––––– ––––––– –––––– –––––––––
 all    builtin local user eigen graph illcond inverse posdef random regprob sparse symmetric
 
 Suite Sparse of
 –––––––––––– ––––
 2770         2833
 
-MatrixMarket of 
+MatrixMarket of
 –––––––––––– –––
 488          498
 
@@ -320,8 +321,8 @@ We can generate a 4-by-4 Hilbert matrix by typing
 ```julia
 julia> matrixdepot("hilb", 4)
 4x4 Array{Float64,2}:
- 1.0       0.5       0.333333  0.25    
- 0.5       0.333333  0.25      0.2     
+ 1.0       0.5       0.333333  0.25
+ 0.5       0.333333  0.25      0.2
  0.333333  0.25      0.2       0.166667
  0.25      0.2       0.166667  0.142857
 ```
@@ -360,7 +361,7 @@ We can also specify the data type for locally generated matrices.
 julia> matrixdepot("hilb", Float16, 5, 3)
 5x3 Array{Float16,2}:
  1.0      0.5      0.33325
- 0.5      0.33325  0.25   
+ 0.5      0.33325  0.25
  0.33325  0.25     0.19995
  0.25     0.19995  0.16663
  0.19995  0.16663  0.14282
@@ -429,30 +430,29 @@ and define [new groups of matrices](http://matrixdepotjl.readthedocs.org/en/late
 
 ## References
 
-- Weijian Zhang and Nicholas J. Higham,
+* Weijian Zhang and Nicholas J. Higham,
   "Matrix Depot: An Extensible Test Matrix Collection for Julia",
   *PeerJ Comput. Sci.*, 2:e58 (2016),
   [[pdf]](https://peerj.com/articles/cs-58/)
 
-- Nicholas J. Higham,
+* Nicholas J. Higham,
   "Algorithm 694, A Collection of Test Matrices in MATLAB",
   *ACM Trans. Math. Software*,
   vol. 17. (1991), pp 289-305
   [[pdf]](http://www.maths.manchester.ac.uk/~higham/narep/narep172.pdf)
   [[doi]](https://dx.doi.org/10.1145/114697.116805)
-
-- T.A. Davis and Y. Hu,
+* T.A. Davis and Y. Hu,
   "The University of Florida Sparse Matrix Collection",
   *ACM Transaction on Mathematical Software*,
   vol. 38, Issue 1, (2011), pp 1:1-1:25
   [[pdf]](http://www.cise.ufl.edu/research/sparse/techreports/matrices.pdf)
 
-- R.F. Boisvert, R. Pozo, K. A. Remington, R. F. Barrett, & J. Dongarra,
+* R.F. Boisvert, R. Pozo, K. A. Remington, R. F. Barrett, & J. Dongarra,
   " Matrix Market: a web resource for test matrix collections",
   *Quality of Numerical Software* (1996) (pp. 125-137).
   [[pdf]](http://www.netlib.org/utk/people/JackDongarra/pdf/matrixmarket.pdf)
 
-- Per Christian Hansen,
+* Per Christian Hansen,
   "Test Matrices for Regularization Methods",
   *SIAM Journal on Scientific Computing*,
   vol. 16, 2, (1995) pp.506-512.

src/data.jl

@@ -116,9 +116,9 @@ const UF_REMOTE = TURemoteType(RemoteParameters(
                    ))
 
 const MM_REMOTE = MMRemoteType(RemoteParameters(
-                    "http://math.nist.gov/MatrixMarket",
-                    "ftp://math.nist.gov/pub/MatrixMarket2",
-                    "http://math.nist.gov/MatrixMarket/matrices.html",
+                    "https://math.nist.gov/MatrixMarket",
+                    "https://math.nist.gov/pub/MatrixMarket2",
+                    "https://math.nist.gov/MatrixMarket/matrices.html",
                     """<TITLE>The Matrix Market Matrices by Name</TITLE>""",
                     ("M", """<A HREF="/MatrixMarket/data/""", 2, ".html", 3, nothing),
                     ".mtx.gz"

src/downloadmm.jl

@@ -36,7 +36,7 @@ function parse_headerinfo(akku::Dict{AbstractString,AbstractString}, count::Inte
     nnz = toint("nonzeros")
     kind = get(akku, "kind", "")
     datestr = get(akku, "date", "0")
-    date = match(r"^\d+$", datestr) != nothing ? parse(Int, datestr) : 0
+    date = match(r"^\d+$", datestr) !== nothing ? parse(Int, datestr) : 0
     id, MetaInfo(m, n, nnz, 0, kind, date, "", "", "", "", "")
 end
 
@@ -53,7 +53,7 @@ function extract_names(db::MatrixDatabase, matrices::AbstractString)
             end
             _, grepex, spquote, ending, parts, regexinf = remote.params.scan
             m = regexinf === nothing ? nothing : match(regexinf, line)
-            if m != nothing
+            if m !== nothing
                 pname = length(m.captures) == 2 ? m.captures[1] : "id"
                 akku[pname] = m.captures[end]
             end

src/markdown.jl

@@ -30,7 +30,7 @@ function mdinfo(data::GeneratedMatrixData)
     md = Docs.doc(data.func)
     # As md is cached internally, need to make copies
     mdh, md = _mdheader(md, nothing, md)
-    if mdh != nothing
+    if mdh !== nothing
         mdh, md = Markdown.Header(copy(mdh.text)), copy(md)
         push!(mdh.text, " ($(data.name))")
         md.content[1] = mdh

src/matrixmarket.jl

@@ -334,7 +334,7 @@ function push_hdr!(hdr, line::AbstractString, field::Symbol)
     end
     reg = r"^% *([^:[]+): *(.*)$"
     regtitle = r"^% *\[([^]]*)]"
-    if (m = match(reg, line)) != nothing
+    if (m = match(reg, line)) !== nothing
         s = Symbol(m[1])
         if s in (:name, :kind, :ed, :fields, :author, :date)
             field = s
@@ -343,7 +343,7 @@ function push_hdr!(hdr, line::AbstractString, field::Symbol)
         elseif s == :notes
             field = s
         end
-    elseif (m = match(regtitle, line)) != nothing
+    elseif (m = match(regtitle, line)) !== nothing
         field = :title
         value = m[1]
         hdr[field] = value

test/download.jl

@@ -17,7 +17,7 @@ import MatrixDepot: load, loadinfo, loadsvd
                         "Harwell-Boeing/smtape/bp___200", "Pajek/Journals"]
 
 # read data
-@test matrixdepot("HB/1138_bus") != nothing
+@test matrixdepot("HB/1138_bus") !== nothing
 @test mdlist("**/1138_bus") == ["HB/1138_bus", "Harwell-Boeing/psadmit/1138_bus"]
 @test string(mdinfo("Harwell-Boeing/psadmit/662_bus")) ==
         "# Harwell-Boeing/psadmit/662_bus\n\n" *
@@ -33,8 +33,8 @@ import MatrixDepot: load, loadinfo, loadsvd
 @test_throws DataError MatrixDepot.metareader(mdopen("that is nothing"))
 
 @test load("Bates/C*") == 2
-@test mdinfo("Bates/Chem97Zt") != nothing
-@test matrixdepot("Bates/Chem97Zt") != nothing
+@test mdinfo("Bates/Chem97Zt") !== nothing
+@test matrixdepot("Bates/Chem97Zt") !== nothing
 @test "Bates/Chem97Zt" in mdlist(isloaded)
 @test length(mdlist(isloaded)) == 6
 
@@ -67,7 +67,7 @@ A2 = mdesc.A
 
 # read a format array file
 @test MatrixDepot.mmreadheader(abspath(MatrixDepot.matrixfile(mdesc.data),
-                                       "..", string("cavity14_b.mtx"))) != nothing
+                                       "..", string("cavity14_b.mtx"))) !== nothing
 
 mdesc = mdopen("blur", 10, false)
 @test mdesc.A isa AbstractMatrix

test/include_generator.jl

@@ -22,7 +22,7 @@ MatrixDepot.publish_user_generators()
 
 n = rand(1:8)
 @test matrixdepot("randsym", n) !== nothing
-@test mdinfo("randsym") != nothing
+@test mdinfo("randsym") !== nothing
 @test "randsym" in MatrixDepot.mdlist(:random)
 @test "randsym" in MatrixDepot.mdlist(:symmetric)
 

test/number.jl

@@ -1,3 +1,3 @@
 n = rand(1:38)
-@test mdinfo(builtin(n)) != nothing
-@test mdinfo(builtin(1:n)) != nothing
+@test mdinfo(builtin(n)) !== nothing
+@test mdinfo(builtin(1:n)) !== nothing

test/property.jl

@@ -1,4 +1,4 @@
-@test mdinfo(:symmetric | :posdef) != nothing
+@test mdinfo(:symmetric | :posdef) !== nothing
 
-@test mdinfo(isloaded) != nothing
+@test mdinfo(isloaded) !== nothing
 

test/regu.jl

@@ -3,10 +3,10 @@ n = 7 # rand(1:10)
 r = mdopen("deriv2", n, false)
 @test r !== nothing && r.A !== nothing
 rf32 = mdopen("deriv2", Float32, n, false)
-@test rf32 !== nothing && rf32.A != nothing
+@test rf32 !== nothing && rf32.A !== nothing
 
 r2 = mdopen("deriv2", Float32, n, 2, false)
-@test r2 !== nothing && r2.b != nothing
+@test r2 !== nothing && r2.b !== nothing
 @test mdopen("deriv2", Float32, (n ÷ 2) * 2, 3, false).A !== nothing
 
 @test_throws ArgumentError matrixdepot("deriv2", Float64, n, 4, false)

test/runtests.jl

@@ -46,7 +46,7 @@ include("generators.jl")
     println("mv $xdir $xtmpdir")
     mv(xdir, xtmpdir, force=true)
     toggle_db()
-    @test mdopen(sp(1)) != nothing
+    @test mdopen(sp(1)) !== nothing
     mv(xtmpdir, xdir, force=true)
 end
 

test/test_rando.jl

@@ -5,7 +5,7 @@ A = matrixdepot("rando", Int, n, 1)
 B = matrixdepot("rando", Int, n, 2)
 C = matrixdepot("rando", Int, n, 3)
 
-for i in length(A)
+for i in 1:length(A)
     @test A[i] == 0 || A[i] == 1
 end