[Caml-list] Attn: Development Editor, Latest OCaml Weekly News

[Alan Schmitt <alan.schmitt@polytechnique.org>]

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Hello

Here is the latest OCaml Weekly News, for the week of November 09 to 16,
2021.

Table of Contents
─────────────────

Early preview of the Algorithmic with OCaml Book
pyml_bindgen: a CLI app to generate Python bindings directly from OCaml value specifications
ocaml-wayland (pure OCaml wayland protocol library)
Set up OCaml 2.0.0-beta6
Set up OCaml 2.0.0-beta7
Set up OCaml 2.0.0-beta8
phylogenetics, a library for molecular evolution
release of svmwrap: a wrapper around libsvm-tools
GeoPub - A XMPP web client
Old CWN


Early preview of the Algorithmic with OCaml Book
════════════════════════════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/early-preview-of-the-algorithmic-with-ocaml-book/8785/1>


Damien Guichard announced
─────────────────────────

  Please report bugs, bad English & nonsenses.  But do not report
  omissions (it is work-in-progress plus it's not an ocaml bible).

  <https://www.cjoint.com/c/KKjulI1Dx03>

  Why the book is not bottom up, instead some concepts are used without
  explained ?

  • Because some notions (what is the `unit' type ? what is a queue ?)
    are considered easy-enough to go without saying.

  What will be in the missing chapter 6 ?

  • Type polymorphism, universal quantification, `Stdlib.compare', weak
    polymorphism, constrained polymorphism, phantom types, type
    variance.

  What will be in the chapters 12 and more ?
  • High performance lexing
  • Recursive-descent parsing
  • The art of searching
  • Detailed construction of the ERic 0.3 application

  Will the source files go to a repository ?

  • No. The source files are already included in the zip archive.


pyml_bindgen: a CLI app to generate Python bindings directly from OCaml value specifications
════════════════════════════════════════════════════════════════════════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-pyml-bindgen-a-cli-app-to-generate-python-bindings-directly-from-ocaml-value-specifications/8786/1>


Ryan Moore announced
────────────────────

  I wanted to announce the first release of [pyml_bindgen], a CLI app
  for generating Python bindings using [pyml] directly from OCaml value
  specifications.

  Manually writing bindings to Python libraries can get tedious pretty
  quickly.  `pyml_bindgen' aims to help you avoid a lot of the
  repetitive work when binding Python libraries by letting you focus on
  the OCaml side of things and (mostly) not worrying about the
  implementation of the pyml bindings.


[pyml_bindgen] <https://github.com/mooreryan/ocaml_python_bindgen>

[pyml] <https://github.com/thierry-martinez/pyml/>

Quick start
╌╌╌╌╌╌╌╌╌╌╌

  First, install `pyml_bindgen'.  It is available on [Opam].

  ┌────
  │ $ opam install pyml_bindgen
  └────

  Say you have a Python class you want to bind and use in OCaml.
  (Filename: `adder.py')

  ┌────
  │ class Adder:
  │     @staticmethod
  │     def add(x, y):
  │ 	return x + y
  └────

  To do so, you write OCaml value specifications for the class and
  methods you want to bind.  (Filename: `val_specs.txt')

  ┌────
  │ val add : x:int -> y:int -> unit -> int
  └────

  Then, you run `pyml_bindgen'.

  ┌────
  │ $ pyml_bindgen val_specs.txt adder Adder --caml-module Adder > lib.ml
  └────

  Now you can use your generated functions in your OCaml code.
  (Filename: `run.ml')

  ┌────
  │ open Lib
  │ 
  │ let () = Py.initialize ()
  │ 
  │ let result = Adder.add ~x:1 ~y:2 ()
  │ 
  │ let () = assert (result = 3)
  └────

  Finally, set up a dune file and run it.

  ┌────
  │ (executable
  │  (name run)
  │  (libraries pyml))
  └────

  ┌────
  │ $ dune exec ./run.exe
  └────


[Opam] <https://opam.ocaml.org/packages/pyml_bindgen/>


Documentation
╌╌╌╌╌╌╌╌╌╌╌╌╌

  For more information on installing and using `pyml_bindgen', check out
  the [docs].  There you will find lots of tips and examples to help you
  get started!


[docs] <https://mooreryan.github.io/ocaml_python_bindgen/>


ocaml-wayland (pure OCaml wayland protocol library)
═══════════════════════════════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-ocaml-wayland-pure-ocaml-wayland-protocol-library/7616/2>


Thomas Leonard announced
────────────────────────

  ocaml-wayland has been very stable over the last few months and so
  I've now released [version 1.0]. The main changes are improved error
  handling and diagnostics.

  I've been using this to write an Xwayland adaptor, which acts as an
  X11 window manager to Xwayland, converting between the two
  protocols. This allows running X11 apps in VMs and having them appear
  alongside other application windows on the host. It can also be used
  to fix other problems, such as support for HiDPI screens and Sway's
  buggy clipboard support:

  <https://roscidus.com/blog/blog/2021/10/30/xwayland/>


[version 1.0]
<https://github.com/talex5/ocaml-wayland/releases/tag/v1.0>


Set up OCaml 2.0.0-beta6
════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-set-up-ocaml-2-0-0-beta6/8795/1>


Sora Morimoto announced
───────────────────────

Changed
╌╌╌╌╌╌╌

  • Unlock opam 2.1 on the Ubuntu and macOS runners.

  <https://github.com/ocaml/setup-ocaml/releases/tag/v2.0.0-beta6>


Set up OCaml 2.0.0-beta7
════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-set-up-ocaml-2-0-0-beta7/8796/1>


Sora Morimoto announced
───────────────────────

Fixed
╌╌╌╌╌

  • Return an empty array to avoid depext failure when depext flags are
    not passed.

  <https://github.com/ocaml/setup-ocaml/releases/tag/v2.0.0-beta7>


Set up OCaml 2.0.0-beta8
════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-set-up-ocaml-2-0-0-beta8/8821/1>


Sora Morimoto announced
───────────────────────

Changed
╌╌╌╌╌╌╌

  • Use 2.1 mode instead of 2.0 mode on the Ubuntu and macOS runners.

  <https://github.com/ocaml/setup-ocaml/releases/tag/v2.0.0-beta8>


phylogenetics, a library for molecular evolution
════════════════════════════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-phylogenetics-a-library-for-molecular-evolution/8812/1>


Philippe announced
──────────────────

  I'm happy to announce the availability on opam of [phylogenetics], a
  bioinformatics library dedicated to [molecular evolution] and
  phylogeny. It provides a few algorithms and data structures that can
  be useful to study how biological sequences like proteins or genes
  have evolved, or to simulate datasets under various evolutionary
  models.

  Comments/questions welcomed on the repo's issue tracker!


[phylogenetics] <https://github.com/biocaml/phylogenetics>

[molecular evolution]
<https://en.wikipedia.org/wiki/Molecular_evolution>


release of svmwrap: a wrapper around libsvm-tools
═════════════════════════════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-release-of-svmwrap-a-wrapper-around-libsvm-tools/8818/1>


UnixJunkie announced
────────────────────

  I am pleased to announce the availability in opam of the svmwrap
  package.  A wrapper around libsvm's svm-train and svm-predict
  executables.  Currently, only regression modeling is supported, using
  the linear, RBF, sigmoid or polynomial kernel.

  <https://github.com/UnixJunkie/svmwrap>

  The quite scary usage looks like this:
  ┌────
  │ usage: svmwrap
  │   -i <filename>: training set or DB to screen
  │   --feats <int>: number of features
  │   [-o <filename>]: predictions output file
  │   [-np <int>]: ncores
  │   [--kernel <string>] choose kernel type {Lin|RBF|Sig|Pol}
  │   [-c <float>]: fix C
  │   [-e <float>]: epsilon in the loss function of epsilon-SVR;
  │   (0 <= epsilon <= max_i(|y_i|))
  │   [-g <float>]: fix gamma (for RBF and Sig kernels)
  │   [-r <float>]: fix r for the Sig kernel
  │   [--iwn]: turn ON instance-wise-normalization
  │   [--scale]: turn ON [0:1] scaling (NOT PRODUCTION READY)
  │   [--no-plot]: no gnuplot
  │   [{-n|--NxCV} <int>]: folds of cross validation
  │   [-q]: quiet
  │   [-v|--verbose]: equivalent to not specifying -q
  │   [--seed <int>]: fix random seed
  │   [-p <float>]: training set portion (in [0.0:1.0])
  │   [--pairs]: read from .AP files (atom pairs; will offset feat. indexes by 1)
  │   [--train <train.liblin>]: training set (overrides -p)
  │   [--valid <valid.liblin>]: validation set (overrides -p)
  │   [--test <test.liblin>]: test set (overrides -p)
  │   [{-l|--load} <filename>]: prod. mode; use trained models
  │   [{-s|--save} <filename>]: train. mode; save trained models
  │   [-f]: force overwriting existing model file
  │   [--scan-c]: scan for best C
  │   [--scan-e <int>]: epsilon scan #steps for SVR
  │   [--scan-g]: scan for best gamma
  │   [--regr]: regression (SVR); also, implied by -e and --scan-e
  │   [--e-range <float>:<int>:<float>]: specific range for e
  │   (semantic=start:nsteps:stop)
  │   [--c-range <float,float,...>] explicit scan range for C
  │   (example='0.01,0.02,0.03')
  │   [--g-range <float,float,...>] explicit range for gamma
  │   (example='0.01,0.02,0.03')
  │   [--r-range <float,float,...>] explicit range for r
  │   (example='0.01,0.02,0.03')
  └────

  For people who know my linwrap opam package (a wrapper around
  liblinear tools), this is quite similar.
  <https://github.com/UnixJunkie/linwrap>


GeoPub - A XMPP web client
══════════════════════════

  Archive:
  <https://discuss.ocaml.org/t/ann-geopub-a-xmpp-web-client/8819/1>


pukkamustard announced
──────────────────────

  I'd like to announce an initial, proof-of-concept release of GeoPub -
  an XMPP web client. Unlike many XMPP clients the focus is not on
  instant messaging but on creating, displaying and managing things such
  as events, maps, information on local organizations and other local
  knowledge (see [the openEngiadina] project for the context).

  This initial release is not really anything useful but a
  proof-of-concept how such an application can be developed using XMPP
  and OCaml. There are many rough edges and broken hacks that need
  fixing. I'd be very grateful for your feedback, thoughts and ideas.

  The source code of the app is on [codeberg] and a pre-built hosted
  version is available [here].

  The application consists of some parts and ideas that I'd like to
  illustrate separately:


[the openEngiadina] <https://openengiadina.net>

[codeberg] <https://codeberg.org/openEngiadina/geopub>

[here] <https://geopub.openengiadina.net/>

ocaml-xmpp
╌╌╌╌╌╌╌╌╌╌

  [ocaml-xmpp] is a XMPP client library for OCaml (documentation
  available [online].


[ocaml-xmpp] <https://codeberg.org/openEngiadina/ocaml-xmpp>

[online] <https://inqlab.net/projects/ocaml-xmpp/>

Reactive
┄┄┄┄┄┄┄┄

  ocaml-xmpp is reactive in the sense that the XMPP connection is
  abstracted as a React event of Stanzas (small pieces of information
  that flow over XMPP):

  ┌────
  │ val stanzas : t -> Stanza.t React.event
  └────

  This React event can be filtered for messages in a specific
  conversation, for example.


Transports
┄┄┄┄┄┄┄┄┄┄

  XMPP works with different transport mechanisms and ocaml-xmpp supports
  this. Currently ocaml-xmpp can be used from Unix with a TCP/SSL
  connection to a XMPP server and from web browsers with a WebSocket
  connection. This is implemented by abstracting the XMPP transport:

  ┌────
  │ module type TRANSPORT = sig
  │   (** {2 Connection} *)
  │ 
  │   type options
  │   (** Additional options that may be passed to the transport *)
  │ 
  │   type t
  │   (** Type of an instantiated connection to an XMPP server *)
  │ 
  │   val connect : host:string -> options -> t Lwt.t
  │ 
  │   val close : t -> unit Lwt.t
  │ 
  │   val closed : t -> unit Lwt.t
  │ 
  │   (** {2 XML Stream} *)
  │ 
  │   type stream
  │ 
  │   val open_stream : t -> to':string -> stream Lwt.t
  │ 
  │   val stream_id : stream -> string Lwt.t
  │ 
  │   val send_xml : stream -> Xmlc.t -> unit Lwt.t
  │ 
  │   val signals : stream -> Xmlc.signal Lwt_stream.t
  │ 
  │   val stop_stream : stream -> unit Lwt.t
  │ end
  └────

  A transport establishes the underlying connection to a server and can
  create XML streams (in XMPP a connection is by multiple XML streams
  sequentially). For technical reasons XML parsing is also handled by
  the transport and a stream of XML signals (element start, data,
  element end) is returned. This is due to the fact that XML parsing in
  XMPP needs to be done slightly differently when using TCP (a single
  XML document over the entire stream) or WebSockets (every WebSocket
  frame is a parse-able XML document).

  The Unix/TCP/SSL transport uses Markup.ml and whereas the WebSocket
  transport uses Xmlm (and Brrr).


Parser combinators for XML
┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄

  For parsing streams of XML signals to OCaml types ocaml-xmpp contains
  a parser combinator helper library: [Xmlc]. This allows parser for XML
  such as this:

  ┌────
  │ <bind xmlns='urn:ietf:params:xml:ns:xmpp-bind'><jid>w4iu4ckn3kjbqvcd@demo.openengiadina.net/z8Pkzfa8</jid></bind>
  └────

  to be parses like this:

  ┌────
  │ Xmlc.Parser.(
  │   element (Ns.bind "bind") (fun _ ->
  │     element (Ns.bind "jid") (fun _ ->
  │       text >>| String.concat "" >>= fun jid_s ->
  │       match Jid.of_string jid_s with
  │       | Some jid -> return jid
  │       | None -> fail_with "invalid JID")))
  └────


[Xmlc] <https://inqlab.net/projects/ocaml-xmpp/xmlc/Xmlc/index.html>


XMPP extensions
┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄

  Inspiration for the scope of the core library is taken from the
  [Strophe] XMPP libraries - everything that does not have directly to
  do with XMPP transport, authentication or stream management is kept
  outside of the core library.

  There are already some "extension" libraries outside of the core for
  useful XMPP features (e.g. [Roster management], [PubSub] and
  [pinging]).

  One thing that I do want to add to the core library is stream
  management according to [XEP-0198]. I expect this addition to change
  the core library API - the API is not stable yet!

  Much inspiration was taken from [Jackline] - an OCaml XMPP client -
  and in particular [this post] on Jackline. Many thanks to @hannes.


[Strophe] <http://strophe.im/>

[Roster management]
<https://inqlab.net/projects/ocaml-xmpp/xmpp/Xmpp_roster/index.html>

[PubSub]
<https://inqlab.net/projects/ocaml-xmpp/xmpp/Xmpp_pubsub/index.html>

[pinging]
<https://inqlab.net/projects/ocaml-xmpp/xmpp/Xmpp_ping/index.html>

[XEP-0198] <https://xmpp.org/extensions/xep-0198.html>

[Jackline] <https://github.com/hannesm/jackline>

[this post] <https://hannes.nqsb.io/Posts/Jackline>


reactor
╌╌╌╌╌╌╌

  GeoPub uses Brr. I had some trouble figuring out a suitable
  "architecture" for managing complex logic and ended up hacking an
  [Elm] inspired helper library: [reactor.mli]. State updates for the
  entire application are then handled in a single [update function].

  I'm not yet very happy with this machinery and I'm pretty sure I'm
  using react in wrong and dangerous ways. I'd be very grateful for
  ideas on how to improve this. THis might be related to this
  discussion:
  <https://discuss.ocaml.org/t/structuring-frp-specifically-note-applications/8645/17>.

  The reason for using React over Note is because ocaml-xmpp uses a lot
  of Lwt and `Lwt_react' provides nice bindings for working with both. I
  guess something similar could be created for Note (e.g. `Lwt_note')
  and I'm open to using Note (also in ocaml-xmpp).


[Elm] <https://elm-lang.org/>

[reactor.mli]
<https://codeberg.org/openEngiadina/geopub/src/branch/main/src/reactor/reactor.mli>

[update function]
<https://codeberg.org/openEngiadina/geopub/src/branch/main/src/geopub/main.ml#L28>


Leaflet
╌╌╌╌╌╌╌

  GeoPub displays a map using the [Leaflet.js] JavaScript
  library. GeoPub contains OCaml bindings to Leaflet using Brr:
  [leaflet.mli]. Writing this was very straightforward and pleasant (I
  like Brr!).

  One issue I have is that the Leaflet map needs to be manipulated very
  imperatively, whereas the rest of the application is much more
  functional. This causes some mismatches. I guess one needs to find a
  way of hiding the impressiveness of Leaflet (e.g. like
  [react-leaflet]).


[Leaflet.js] <https://leafletjs.com/>

[leaflet.mli]
<https://codeberg.org/openEngiadina/geopub/src/branch/main/src/leaflet/leaflet.mli>

[react-leaflet] <https://github.com/PaulLeCam/react-leaflet>


Guix for build and development environments
╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌

  I use [Guix] for providing a build and development environment. With
  guix installed one can run `guix shell' in the GeoPub repository to
  get a reproducible build environment. All dependencies are fetched and
  made available by Guix in this environment (e.g. `ocaml-xmpp' or the
  OCaml compiler).

  I will publish `ocaml-xmpp' on OPAM once the API is more stable and an
  initial release can be made.


[Guix] <https://guix.gnu.org/>


Old CWN
═══════

  If you happen to miss a CWN, you can [send me a message] and I'll mail
  it to you, or go take a look at [the archive] or the [RSS feed of the
  archives].

  If you also wish to receive it every week by mail, you may subscribe
  [online].

  [Alan Schmitt]


[send me a message] <mailto:alan.schmitt@polytechnique.org>

[the archive] <https://alan.petitepomme.net/cwn/>

[RSS feed of the archives] <https://alan.petitepomme.net/cwn/cwn.rss>

[online] <http://lists.idyll.org/listinfo/caml-news-weekly/>

[Alan Schmitt] <https://alan.petitepomme.net/>


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