From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 05 10:28:43 2023 Received: (at submit) by debbugs.gnu.org; 5 Dec 2023 15:28:43 +0000 Received: from localhost ([127.0.0.1]:38079 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXLn-0006Wr-7H for submit@debbugs.gnu.org; Tue, 05 Dec 2023 10:28:43 -0500 Received: from lists.gnu.org ([2001:470:142::17]:53110) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXLl-0006Wf-9j for submit@debbugs.gnu.org; Tue, 05 Dec 2023 10:28:41 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rAXLT-0007gY-LC for guix-patches@gnu.org; Tue, 05 Dec 2023 10:28:24 -0500 Received: from mout02.posteo.de ([185.67.36.66]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rAXLR-0000Dj-Km for guix-patches@gnu.org; Tue, 05 Dec 2023 10:28:23 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 0DACD240103 for ; Tue, 5 Dec 2023 16:28:19 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1701790099; bh=Vkt9C9da5ZOH8R0ddWFpBY1j+jJxFYPmbbv4FCfD9u0=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=j4G8JOgPRnzuknIYjLoV6H0gGZ1MhL2a7PNA90YZaTtBvoLch8NBeqMf6MAzhsIiP QhhyWoY1Yw9mHfT2Y5XfClJ81K1Ei14EK786CzgqO5tNrk4kY1KPeMy3EP70lLV5lG 4dusxxb/wpU+Aaes2ZX+gF8VkelYc0Zn/flLp+31AH+ecPVBR6GomEf47Sq1Yz0u92 Y5nBtUBWY8gPFNo50H5D6nZyar5r1fNXInmmvVS109I5yc4latTIDONO+t5Ztn/ch/ ENqB3+a0r9aCvjF9r8gQ71Xx8AY/v76Y45rTCi+S53jhA1gyt3v7cpx96WMt56UVeV LohJo2Y2k8QYg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Sl4Df0XHPz6tvp; Tue, 5 Dec 2023 16:28:17 +0100 (CET) From: Vinicius Monego To: guix-patches@gnu.org Subject: [PATCH 0/2] Add python-bambi. Date: Tue, 5 Dec 2023 15:28:01 +0000 Message-Id: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.66; envelope-from=monego@posteo.net; helo=mout02.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: Vinicius Monego X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) Bambi is a high-level Bayesian model-building interface for PyMC. Vinicius Monego (2): gnu: Add python-formulae. gnu: Add python-bambi. gnu/packages/statistics.scm | 107 +++++++++++++++++++++++++++++++++--- 1 file changed, 100 insertions(+), 7 deletions(-) base-commit: c15a1cd88f80a90437f4b0159f22dfc84b9e6851 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 05 10:31:01 2023 Received: (at 67643) by debbugs.gnu.org; 5 Dec 2023 15:31:01 +0000 Received: from localhost ([127.0.0.1]:38085 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXO0-0006cV-NW for submit@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:01 -0500 Received: from mout01.posteo.de ([185.67.36.65]:55037) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXNz-0006cE-CQ for 67643@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:00 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 85D09240027 for <67643@debbugs.gnu.org>; Tue, 5 Dec 2023 16:30:42 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1701790242; bh=H/ybwgr4qjwQljlGwUjNn/pBRxMdux3M5dD/ul18fnY=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Sv6kyjqvrbwaleT+iKQTPYifsYyItjRTsjeV8Kj2yzmeIPo26gktvbsna93eJQhq0 iQGZ8YiGyz7KUF/57VpfXd3CWLrX9pzK9Rtmo0LlcmQ3hk91q9X1jwruYRGdamNv7n Zl4d6A/W5K1ZnNtQRnu0pSDXJOUtGUr/RdguZ1g4e0nfyoh1wWgcEq6fWgTq5EfKO4 0TdTOv7TVqFNO2hKyNjMGl1Hqyij3lN+3hkVcGQbyFvFeZPvWUwAeeNx0H6l2e+kd3 XxKeAlm/hfORpF19xCAfJfOlLdh6x1pvOJ59ZD5Ii9KQfJTI2pvkwci+xor7o22iGu JDctpiQQMpKow== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Sl4HP4vWWz6trs; Tue, 5 Dec 2023 16:30:41 +0100 (CET) From: Vinicius Monego To: 67643@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add python-bambi. Date: Tue, 5 Dec 2023 15:30:19 +0000 Message-Id: <758492077c8b05e2aee5aca1726379322bcbb277.1701789886.git.monego@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.6 (/) X-Debbugs-Envelope-To: 67643 Cc: Vinicius Monego X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.6 (-) * gnu/packages/statistics.scm: Sort modules alphabetically. (python-bambi): New variable. Change-Id: I54931227310e3ad3b8d5c9272dcc641877b78bfb --- gnu/packages/statistics.scm | 77 +++++++++++++++++++++++++++++++++---- 1 file changed, 70 insertions(+), 7 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 30c6a9483e..c9a9672a35 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -35,25 +35,26 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages statistics) - #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix hg-download) + #:use-module (guix gexp) #:use-module (guix git-download) + #:use-module (guix hg-download) + #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix build-system ant) #:use-module (guix build-system cmake) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) - #:use-module (guix build-system r) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) - #:use-module (guix build-system trivial) + #:use-module (guix build-system r) #:use-module (guix build-system ruby) + #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) @@ -66,9 +67,10 @@ (define-module (gnu packages statistics) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) - #:use-module (gnu packages gtk) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) + #:use-module (gnu packages graphviz) + #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) @@ -100,7 +102,6 @@ (define-module (gnu packages statistics) #:use-module (gnu packages texinfo) #:use-module (gnu packages time) #:use-module (gnu packages tls) - #:use-module (gnu packages base) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages web) @@ -2266,6 +2267,68 @@ (define-public python-formulae for mixed-effects models.") (license license:expat))) +(define-public python-bambi + (package + (name "python-bambi") + (version "0.13.0") + (source + (origin + (method git-fetch) ;PyPI is missing files required by tests + (uri (git-reference + (url "https://github.com/bambinos/bambi") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hkkw65nbxg15rzp9rc8zxxwsg454hfa5mq853752hp6bp4r7szp")))) + (build-system pyproject-build-system) + (arguments + ;; The tests below use the network, and there's no configuration to + ;; skip the network tests. + (list + #:test-flags + #~(list "--ignore" + "tests/test_aliases.py" + "--ignore" + "tests/test_plots.py" + "-k" + (string-append + "not " + (string-join + (list + "test_logistic_regression_categoric_alternative_samplers" + "test_regression_alternative_samplers" + "test_predict_new_groups" + "test_predict_new_groups_fail" + "test_censored_response" + "test_data_is_copied" + "test_extra_namespace" + "test_predict_offset" + "test_custom_prior" + "test_normal_with_splines" + "test_gamma_with_splines") + " and not "))) + #:phases #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; Some tests require write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs (list python-arviz python-formulae python-graphviz + python-pandas python-pymc)) + (native-inputs (list python-black + python-ipython + python-pylint + python-pytest + python-pytest-cov + python-seaborn)) + (home-page "https://bambinos.github.io/bambi/") + (synopsis "Bayesian Model Building Interface in Python") + (description + "Bambi is a high-level Bayesian model-building interface written in Python. +It's built on top of the PyMC probabilistic programming framework, and is +designed to make it extremely easy to fit mixed-effects models common in +social sciences settings using a Bayesian approach.") + (license license:expat))) + (define-public python-chaospy (package (name "python-chaospy") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 05 10:31:01 2023 Received: (at 67643) by debbugs.gnu.org; 5 Dec 2023 15:31:01 +0000 Received: from localhost ([127.0.0.1]:38087 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXO1-0006cX-BP for submit@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:01 -0500 Received: from mout01.posteo.de ([185.67.36.65]:51261) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXNw-0006c7-2B for 67643@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:00 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id ABBD5240029 for <67643@debbugs.gnu.org>; Tue, 5 Dec 2023 16:30:38 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1701790238; bh=cYdsvbueLyVastPYQYyiHOy6rjxWDcnIvMg7kAv0FG4=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=SutzNsGgZaOEQeVF1yNESSVY859Et+U7oqY05+BFExoVUb2V7XUW5VtyaUyXKvXZP iB9fKcj2hOrazPrZctTQiD9GiTTtYDAtKCxSBPs04N3obgWJ8aApnuVTe/ExWLc3AX 2jYy4l9I1r5sZJDGiJr/h7YMSrNay5kq8zf2QRs9BP/rddmBbXxOniDwOLmElQx+hx aLWaoG4329qrS+wxdJ935vqZQhvV81VNl6Hs78+itWPLT3z5GuWqSSW5pQLQnKFGMS 7gT3gaHFXMFi7tohG2kaBUSjQ5BwXDWnQWBJCYMOX07t5AQo4Xyg+DoNnRMYSx/Qz8 c97ZaNiSUvFgA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Sl4HK5rPJz6trs; Tue, 5 Dec 2023 16:30:37 +0100 (CET) From: Vinicius Monego To: 67643@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add python-formulae. Date: Tue, 5 Dec 2023 15:30:18 +0000 Message-Id: <083385b33f32b09e11ef1bd4e1ce7063de8918fb.1701789886.git.monego@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.6 (/) X-Debbugs-Envelope-To: 67643 Cc: Vinicius Monego X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.6 (-) * gnu/packages/statistics.scm (python-formulae): New variable. Change-Id: I65f5c71fd30679b11fe370372d6992df54d86f19 --- gnu/packages/statistics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 95cc948d9f..30c6a9483e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2236,6 +2236,36 @@ (define-public python-pymc inference (VI) algorithms.") (license license:asl2.0))) +(define-public python-formulae + (package + (name "python-formulae") + (version "0.5.1") + (source (origin + (method git-fetch) ; PyPI is missing files required by tests + (uri (git-reference + (url "https://github.com/bambinos/formulae") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0s22ggsss1zrz3bdw1zm3kwbm07bdlp0v1af8xhw8ymcg9sqcsly")))) + (build-system pyproject-build-system) + (arguments + ;; AssertionError: approx() is not supported in a boolean context. + (list #:test-flags #~(list "-k" "not test_basic and not test_degree"))) + (propagated-inputs (list python-numpy python-pandas python-scipy)) + (native-inputs (list python-black + python-ipython + python-pylint + python-pytest + python-pytest-cov)) + (home-page "https://bambinos.github.io/formulae/") + (synopsis "Formulas for mixed-effects models in Python") + (description + "@code{formulae} is a Python library that implements Wilkinson’s formulas +for mixed-effects models.") + (license license:expat))) + (define-public python-chaospy (package (name "python-chaospy") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 02 15:31:12 2024 Received: (at 67643) by debbugs.gnu.org; 2 Feb 2024 20:31:13 +0000 Received: from localhost ([127.0.0.1]:45581 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rW0Bs-0003jf-IX for submit@debbugs.gnu.org; Fri, 02 Feb 2024 15:31:12 -0500 Received: from mail-lf1-x132.google.com ([2a00:1450:4864:20::132]:57703) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rW0Bp-0003jQ-JF for 67643@debbugs.gnu.org; Fri, 02 Feb 2024 15:31:10 -0500 Received: by mail-lf1-x132.google.com with SMTP id 2adb3069b0e04-511234430a4so4196928e87.3 for <67643@debbugs.gnu.org>; Fri, 02 Feb 2024 12:30:58 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1706905852; x=1707510652; darn=debbugs.gnu.org; h=to:subject:message-id:date:from:mime-version:from:to:cc:subject :date:message-id:reply-to; bh=kLqk7/7Uhx7lvxWP7iJ2PBzEWj+LB6r0pu1V/oFLsnA=; b=jwLnGrenqH8+DojPlbIK3+cW8/EfOO7Z/LSiik03dYoZJR0bj+iPDj2XFB5wXqAcAb mehZrOWCZBSc2z4NfIF/1BFDfZ2eqr0ADCfrBwuUwTaO0ItVwIclNs61j9sTdRqyTQeH TyfEQcSqiwb25vnK8qlhqmi5oD0X2D7x0W24n3wLWXONpu5TGfFDiTUN7Uc6m35xw2c/ pRykpF6jXHZ+RH+Y03JmmhgxQt/PXvSmaCVjXP4MqAHYNPqVncRSSVboSfXBZcBFz/VR krOH0BwIghC92L1m9cGKgZ2zYmDw8LpyByJbWTICkRF8gb9h/dW8ri6kNEVRhwWbTnjb lMcw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1706905852; x=1707510652; h=to:subject:message-id:date:from:mime-version:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=kLqk7/7Uhx7lvxWP7iJ2PBzEWj+LB6r0pu1V/oFLsnA=; b=P42r3WxX+gXuZiCw97XW3WiBRp1pXOw5Su3J8fQMDaymmo+4B+n78H+TF1Hg0BN7j8 fClieE+l1jESaWXKktEV/kmxRDIcs3riPl0X57CZf0maTPTUbOHfYv8L0KjBtrkZrR7P tPXDiunxoOHakIr0HfdPdEjSr7QJwTnwDLsYZtPm7LthO/xMol/hQJt6t2XDY2xbjHjp WrFJMEBd0Zwfr4Z6EIodlv7f3ztwA8bGRyxY/JER3kWeFxrKlA1VcZqsxUBIGQtAp2jv sgEmMvYxz3DOp/aLL1EKAX++caDOJsCdkrhRsb7CJ/+1i/iRFPF4TGMPDmkZckTla0Zq ZQMw== X-Gm-Message-State: AOJu0YyZl0DIX/iBSn654v0+DeJlkHOPWhDZVKuF4GlOfSQJq6Vqvbhq D9qLKbTHq/S4S8YgJiujhcWbQFkFyug8vtdJBLh3bfj5QjpQjPTGF8OLD03BiDG167pn70jkVpY wVhFE3nmDiTM0J8YoQRCsr+YIiT7wdLBG3AY= X-Google-Smtp-Source: AGHT+IEjp/pZKCnYbG/RFpeRPaOK7ZFg2KKUWzMM0vFovZKo+Wg3VYRCip+HVGerIMHcEYW/jtlHkgs09St+S2Fyl5o= X-Received: by 2002:a05:6512:3742:b0:510:128b:4d8e with SMTP id a2-20020a056512374200b00510128b4d8emr4440158lfs.7.1706905852139; Fri, 02 Feb 2024 12:30:52 -0800 (PST) MIME-Version: 1.0 From: Sharlatan Hellseher Date: Fri, 2 Feb 2024 20:30:41 +0000 Message-ID: Subject: [PATCH 0/2] Add python-bambi. To: 67643@debbugs.gnu.org Content-Type: multipart/alternative; boundary="000000000000fb5ddd06106bfce0" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 67643 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --000000000000fb5ddd06106bfce0 Content-Type: text/plain; charset="UTF-8" Hi, Thank you for the patches! >From a quick glance they look good, I am about to check upstream license(s) and any hidden bundled code/libraries. One neat pick. You combined adding new package with module house keeping changes (sorting use-module alphabetically), to make a review smoother may you split it into 3 please, with house keeping part as separate patch? Looking forward for v2! Thanks, Oleg --000000000000fb5ddd06106bfce0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

Thank yo= u for the patches!

From = a quick glance they look good,=C2=A0 I am about to check
upstream license(s) and any hidden bundled code/libraries.

One neat pick. You combined adding = new package with module
house keeping changes (sorti= ng use-module alphabetically), to
make a review smoo= ther may you split it into 3 please, with house
keep= ing part as separate patch?

Looking forward for v2!

Thanks,
Oleg
--000000000000fb5ddd06106bfce0--