GNU bug report logs - #56426
[PATCH 0/6] Add Julia CSV

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/6] Add Julia CSV
Date: Wed,  6 Jul 2022 20:05:37 +0200

Hi,

This series adds Julia CSV reader/writer.  Well, 'CSV.Chunks' fails so then
the 2 related tests.  I have no clue what could be wrong.  Therefore, I have
disabled these two ones.

I am currently checking some packages for i686-linux but the issues, if any,
can be addressed later.  Having the feedback from the build will help.


Cheers,
simon



zimoun (6):
  gnu: julia-parsers: Update to 2.2.4.
  gnu: Add julia-inlinestrings.
  gnu: julia-json: Update to 0.21.3.
  gnu: julia-weakrefstrings: Update to 1.4.0.
  gnu: Add julia-sentinelarrays.
  gnu: Add julia-csv.

 gnu/packages/julia-xyz.scm | 103 ++++++++++++++++++++++++++++++++++---
 1 file changed, 97 insertions(+), 6 deletions(-)


base-commit: 111bdcff48902457a7218f7ef8a80ad3dfaac3d1
-- 
2.36.0

Message #8 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/6] gnu: Add julia-inlinestrings.
Date: Wed,  6 Jul 2022 20:06:40 +0200

* gnu/packages/julia-xyz.scm (julia-inlinestrings): New variable.
---
 gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c6f3ad5d61..49816507bd 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2847,6 +2847,32 @@ (define-public julia-inifile
 interfaces with @file{.ini} files.")
     (license license:expat)))
 
+(define-public julia-inlinestrings
+  (package
+    (name "julia-inlinestrings")
+    (version "1.1.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaStrings/InlineStrings.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1dcdpxlphjliqlnkcri7mhg9bqqzpsdj80h9gkw8xhzr3ls473zr"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-parsers))
+    (home-page "https://github.com/JuliaStrings/InlineStrings.jl")
+    (synopsis "Fixed-width string types")
+    (description "This package provides a set of custom string types of
+various fixed sizes.  Each inline string is a custom primitive type and can
+benefit from being stack friendly by avoiding allocations/heap tracking in the
+GC.  When used in an array, the elements are able to be stored inline since
+each one has a fixed size.  Currently support inline strings from 1 byte up to
+255 bytes.")
+    (license license:expat)))
+
 (define-public julia-interpolations
   (package
     (name "julia-interpolations")
-- 
2.36.0

Message #11 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/6] gnu: julia-parsers: Update to 2.2.4.
Date: Wed,  6 Jul 2022 20:06:39 +0200

* gnu/packages/julia-xyz.scm (julia-parsers): Update to 2.2.4.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 56cff1ea6f..c6f3ad5d61 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3946,7 +3946,7 @@ (define-public julia-parameters
 (define-public julia-parsers
   (package
     (name "julia-parsers")
-    (version "1.1.0")
+    (version "2.2.4")
     (source
      (origin
        (method git-fetch)
@@ -3955,7 +3955,7 @@ (define-public julia-parsers
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1gz3drd5334xrbx2ms33hiifkd0q1in4ywc92xvrkq3xgzdjqjdk"))))
+        (base32 "09v2x9yd1wdp74hzsf6218dpamlf2hb5nkmixqb4bc53ll8hpw4i"))))
     (build-system julia-build-system)
     (home-page "https://github.com/JuliaData/Parsers.jl")
     (synopsis "Fast parsing machinery for basic types in Julia")
-- 
2.36.0

Message #14 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 5/6] gnu: Add julia-sentinelarrays.
Date: Wed,  6 Jul 2022 20:06:43 +0200

* gnu/packages/julia-xyz.scm (julia-sentinelarrays): New variable.
---
 gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 7491ee3f5d..c53efb3d76 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4797,6 +4797,27 @@ (define-public julia-scratch
 files that the user must interact with through a file browser.")
     (license license:expat)))
 
+(define-public julia-sentinelarrays
+  (package
+    (name "julia-sentinelarrays")
+    (version "1.3.13")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaData/SentinelArrays.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1h3vpz7xskbf2a60imdg0irwh9bybkahjpnb6b3wyk0j9a97nqkr"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaData/SentinelArrays.jl")
+    (synopsis "Array types using sentinel values")
+    (description "This package provides @code{SentinelArray{T}} that wraps an
+@code{AbstractArray} of type @code{T}, and accepts a sentinel and value
+argument.")
+    (license license:expat)))
+
 (define-public julia-showoff
   (package
     (name "julia-showoff")
-- 
2.36.0

Message #17 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 3/6] gnu: julia-json: Update to 0.21.3.
Date: Wed,  6 Jul 2022 20:06:41 +0200

* gnu/packages/julia-xyz.scm (julia-json): Update to 0.21.3.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 49816507bd..ac7d5fd07e 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3112,7 +3112,7 @@ (define-public julia-jive
 (define-public julia-json
   (package
     (name "julia-json")
-    (version "0.21.1")
+    (version "0.21.3")
     (source
      (origin
        (method git-fetch)
@@ -3121,7 +3121,7 @@ (define-public julia-json
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m"))))
+        (base32 "1l2p852sxq6h5fif3dqshvbw17gb06jmq2nkr88spvp7s0n0nslz"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-datastructures
-- 
2.36.0

Message #20 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 4/6] gnu: julia-weakrefstrings: Update to 1.4.0.
Date: Wed,  6 Jul 2022 20:06:42 +0200

* gnu/packages/julia-xyz.scm (julia-weakrefstrings): Update to 1.4.0.
---
 gnu/packages/julia-xyz.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index ac7d5fd07e..7491ee3f5d 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5651,7 +5651,7 @@ (define-public julia-versionparsing
 (define-public julia-weakrefstrings
   (package
     (name "julia-weakrefstrings")
-    (version "1.1.0")
+    (version "1.4.0")
     (source
       (origin
         (method git-fetch)
@@ -5660,10 +5660,11 @@ (define-public julia-weakrefstrings
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219"))))
+         (base32 "1ca94bpsjqrap2y9wlixspnisfkcms7aax0kpv7yn0v2vs9481wk"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-dataapi
+           julia-inlinestrings
            julia-parsers))
     (home-page "https://github.com/JuliaData/WeakRefStrings.jl")
     (synopsis "Efficient string representation and transfer in Julia")
-- 
2.36.0

Message #23 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 6/6] gnu: Add julia-csv.
Date: Wed,  6 Jul 2022 20:06:44 +0200

* gnu/packages/julia-xyz.scm (julia-csv): New variable.
---
 gnu/packages/julia-xyz.scm | 43 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c53efb3d76..e5b159245c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1119,6 +1119,49 @@ (define-public julia-crayons
 styles available to terminals.")
     (license license:expat)))
 
+(define-public julia-csv
+  (package
+    (name "julia-csv")
+    (version "0.10.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaData/CSV.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "15kjh5wa6ravb10n9n9bsh7ggmarqmw8s57p35l4b3dqk9d8qafh"))))
+    (build-system julia-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'fix-reference-to-cat
+                 (lambda _
+                   (substitute* "test/basics.jl"
+                     ;; XXXX: Test fail to read using CVS.Chunk; raising:
+                     ;; ArgumentError: unable to iterate chunks from input file source
+                     ;; Disable and the two tests using it.
+                     (("chunks = CSV.Chunks") "# chunks = CSV.Chunks")
+                     (("@test sum\\(length, chunks\\) == 10000")
+                      "# @test sum(length, chunks) == 10000")
+                     (("@test Tables.partitions\\(chunks\\) === chunks")
+                      "# @test Tables.partitions(chunks) === chunks")))))))
+    (propagated-inputs
+     (list julia-codeczlib
+           julia-filepathsbase
+           julia-inlinestrings
+           julia-parsers
+           julia-pooledarrays
+           julia-sentinelarrays
+           julia-tables
+           julia-weakrefstrings))
+    (home-page "https://github.com/JuliaData/CSV.jl")
+    (synopsis "Fast and flexible delimited-file reader/writer")
+    (description "This package provides reader/writer for delimited text data,
+as comma-delimited (csv), tab-delimited (tsv), or otherwise.")
+    (license license:expat)))
+
 (define-public julia-dataapi
   (package
     (name "julia-dataapi")
-- 
2.36.0

Message #26 received at 56426 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 56426 <at> debbugs.gnu.org
Cc: efraim <at> flashner.co.il
Subject: Re: bug#56426: [PATCH 0/6] Add Julia CSV
Date: Fri, 08 Jul 2022 09:51:59 +0200

Hi,

On Wed, 06 Jul 2022 at 20:05, zimoun <zimon.toutoune <at> gmail.com> wrote:

> This series adds Julia CSV reader/writer.  Well, 'CSV.Chunks' fails so then
> the 2 related tests.  I have no clue what could be wrong.  Therefore, I have
> disabled these two ones.

Well, I have no clue why CVS.Chunks fails:

--8<---------------cut here---------------start------------->8---
 :col1  PosLenStringCSV.File basics: Error During Test at
/gnu/store/…-julia-csv-0.10.4/share/julia/loadpath/CSV/test/basics.jl:20
  Got exception outside of a @test
  ArgumentError: unable to iterate chunks from input file source
  Stacktrace:
    [1] CSV.Chunks(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Int64,
footerskip::Int64, transpose::Bool, comment::Nothing, ignoreemptyrows::Bool, ignoreemptylines::Nothing,
select::Nothing, drop::Nothing, limit::Nothing, buffer_in_memory::Bool, ntasks::Nothing, tasks::Nothing,
rows_to_check::Int64, lines_to_check::Nothing, missingstrings::Vector{String}, missingstring::String,
delim::Nothing, ignorerepeated::Bool, quoted::Bool, quotechar::Char, openquotechar::Nothing,
closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8,
truestrings::Vector{String}, falsestrings::Vector{String}, stripwhitespace::Bool, type::Nothing, types::Nothing,
typemap::Dict{Type, Type}, pool::Tuple{Float64, Int64}, downcast::Bool, lazystrings::Bool,
stringtype::Type{PosLenString}, strict::Bool, silencewarnings::Bool, maxwarnings::Int64, debug::Bool,
parsingdebug::Bool, validate::Bool)
      @ CSV /gnu/store/…-julia-csv-0.10.4/share/julia/loadpath/CSV/src/chunks.jl:81
    [2] macro expansion
      @ /gnu/store/…-julia-csv-0.10.4/share/julia/loadpath/CSV/test/basics.jl:510 [inlined]
--8<---------------cut here---------------end--------------->8---

because it just reads:

--8<---------------cut here---------------start------------->8---
510: chunks = CSV.Chunks(joinpath(dir, "promotions.csv"); stringtype=PosLenString)
511: @test sum(length, chunks) == 10000
512: @test Tables.partitions(chunks) === chunks
--8<---------------cut here---------------end--------------->8---

Well, these 3 lines and 2 tests are thus bypassed over the thousands of
other tests. :-)


> I am currently checking some packages for i686-linux but the issues, if any,
> can be addressed later.  Having the feedback from the build will help.

Well, the current situation of i686 is bad [1,2] but unrelated to this
patch series.  Let merge this series which is perfectly fine for x86_64
and then fix the other arch as i686.

1: <https://ci.guix.gnu.org/build/1089455/details>
2: <https://ci.guix.gnu.org/build/1089455/log/raw>


Cheers,
simon

Message #31 received at 56426-done <at> debbugs.gnu.org (full text, mbox):

From: Efraim Flashner <efraim <at> flashner.co.il>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 56426-done <at> debbugs.gnu.org
Subject: Re: [bug#56426] [PATCH 0/6] Add Julia CSV
Date: Mon, 11 Jul 2022 13:08:47 +0300

[Message part 1 (text/plain, inline)]

On Wed, Jul 06, 2022 at 08:05:37PM +0200, zimoun wrote:
> Hi,
> 
> This series adds Julia CSV reader/writer.  Well, 'CSV.Chunks' fails so then
> the 2 related tests.  I have no clue what could be wrong.  Therefore, I have
> disabled these two ones.
> 
> I am currently checking some packages for i686-linux but the issues, if any,
> can be addressed later.  Having the feedback from the build will help.
> 
> 
> Cheers,
> simon
> 
> 
> 
> zimoun (6):
>   gnu: julia-parsers: Update to 2.2.4.
>   gnu: Add julia-inlinestrings.
>   gnu: julia-json: Update to 0.21.3.
>   gnu: julia-weakrefstrings: Update to 1.4.0.
>   gnu: Add julia-sentinelarrays.
>   gnu: Add julia-csv.
> 
>  gnu/packages/julia-xyz.scm | 103 ++++++++++++++++++++++++++++++++++---
>  1 file changed, 97 insertions(+), 6 deletions(-)
> 
> 
> base-commit: 111bdcff48902457a7218f7ef8a80ad3dfaac3d1
> -- 
> 2.36.0
> 

It looks fine to me as it is. I'm also not sure why that particular test
is failing but I think it's fine to skip it for now.

I've pushed the patches.

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[signature.asc (application/pgp-signature, inline)]

Message #34 received at 56426-done <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Efraim Flashner <efraim <at> flashner.co.il>, zimoun <zimon.toutoune <at> gmail.com>,
 56426-done <at> debbugs.gnu.org
Subject: Re: [bug#56426] [PATCH 0/6] Add Julia CSV
Date: Mon, 11 Jul 2022 13:42:42 +0200

Hi,


On Mon, 11 Jul 2022 at 12:09, Efraim Flashner <efraim <at> flashner.co.il> wrote:

> I've pushed the patches.

Thanks.

Cheers,
simon

PS:
I have noticed the general status of Julia for i686-linux is really
bad; I do not have time to investigate more; maybe on spetember.

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