Package: guix-patches;
Reported by: Vinicius Monego <monego <at> posteo.net>
Date: Sat, 20 May 2023 23:12:02 UTC
Severity: normal
Tags: patch
Done: Vinicius Monego <monego <at> posteo.net>
Bug is archived. No further changes may be made.
To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 63619 in the body.
You can then email your comments to 63619 AT debbugs.gnu.org in the normal way.
Toggle the display of automated, internal messages from the tracker.
View this report as an mbox folder, status mbox, maintainer mbox
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:12:02 GMT) Full text and rfc822 format available.Vinicius Monego <monego <at> posteo.net>:guix-patches <at> gnu.org.
(Sat, 20 May 2023 23:12:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: guix-patches <at> gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 0/9] Add PyMC. Date: Sat, 20 May 2023 23:10:58 +0000
This patchset adds the PyMC probabilistic programming package. Vinicius Monego (9): gnu: Add python-vega-datasets. gnu: Add python-altair. gnu: Add python-einops. gnu: python-xarray: Update to 2023.5.0. gnu: Add python-xarray-einstats. gnu: Add python-arviz. gnu: Add python-fastprogress. gnu: Add python-pytensor. gnu: Add python-pymc. gnu/packages/python-science.scm | 150 +++++++++++++++++++++++++++++--- gnu/packages/python-xyz.scm | 26 ++++++ gnu/packages/statistics.scm | 140 +++++++++++++++++++++++++++++ 3 files changed, 306 insertions(+), 10 deletions(-) -- 2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:02 GMT) Full text and rfc822 format available.Message #8 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 1/9] gnu: Add python-vega-datasets. Date: Sat, 20 May 2023 23:12:33 +0000
* gnu/packages/statistics.scm (python-vega-datasets): New variable.
---
gnu/packages/statistics.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 13232a00e3..d42c6baed6 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2062,6 +2062,26 @@ (define-public r-xtable
"This package provides tools to export R data as LaTeX and HTML tables.")
(license license:gpl2+)))
+(define-public python-vega-datasets
+ (package
+ (name "python-vega-datasets")
+ (version "0.9.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "vega_datasets" version))
+ (sha256
+ (base32
+ "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ `(#:tests? #f)) ; this is a data-only package, so no tests
+ (propagated-inputs (list python-pandas))
+ (home-page "https://github.com/altair-viz/vega_datasets")
+ (synopsis "Example datasets used by Vega-related projects")
+ (description "This package provides a collection of datasets used in Vega
+and Vega-Lite examples.")
+ (license license:expat)))
+
(define-public python-hdmedians
(package
(name "python-hdmedians")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:02 GMT) Full text and rfc822 format available.Message #11 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 2/9] gnu: Add python-altair. Date: Sat, 20 May 2023 23:12:34 +0000
* gnu/packages/statistics.scm (python-altair): New variable.
---
gnu/packages/statistics.scm | 39 +++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d42c6baed6..574790731e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -85,6 +85,7 @@ (define-module (gnu packages statistics)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
@@ -2082,6 +2083,44 @@ (define-public python-vega-datasets
and Vega-Lite examples.")
(license license:expat)))
+(define-public python-altair
+ (package
+ (name "python-altair")
+ (version "5.0.0")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/altair-viz/altair")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "11j7v2s25xwz3qdjbbps3ma2dd68cr87vxn22x9fyfzgbs9pc7mx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; test_render_examples_to_chart opens an external connection.
+ ;; test_save_html introduces a circular dependency on altair-viewer.
+ (list #:test-flags #~(list "-k" (string-append
+ "not test_render_examples_to_chart"
+ " and not test_save_html"))))
+ (propagated-inputs (list python-jinja2
+ python-jsonschema
+ python-numpy
+ python-pandas
+ python-toolz
+ python-typing-extensions))
+ (native-inputs (list python-black
+ python-hatchling
+ python-ipython
+ python-m2r
+ python-pytest
+ python-vega-datasets))
+ (home-page "https://altair-viz.github.io/")
+ (synopsis "Declarative statistical visualization library for Python")
+ (description
+ "Vega-Altair is a declarative statistical visualization library for Python.")
+ (license license:expat)))
+
(define-public python-hdmedians
(package
(name "python-hdmedians")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:03 GMT) Full text and rfc822 format available.Message #14 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 3/9] gnu: Add python-einops. Date: Sat, 20 May 2023 23:12:35 +0000
* gnu/packages/python-science.scm (python-einops): New variable.
---
gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7d3319e367..91c3904783 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -669,6 +669,40 @@ (define-public python-geosketch
necessary for reproducing the experiments in the paper.")
(license license:expat)))
+(define-public python-einops
+ (package
+ (name "python-einops")
+ (version "0.6.1")
+ (source (origin
+ (method git-fetch) ;PyPI misses .ipynb files required for tests
+ (uri (git-reference
+ (url "https://github.com/arogozhnikov/einops")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1h8p39kd7ylg99mh620xr20hg7v78x1jnj6vxwk31rlw2dmv2dpr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-backend
+ (lambda _
+ ;; Einops supports different backends, but we test
+ ;; only NumPy for availability and simplicity.
+ (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
+ (native-inputs (list jupyter
+ python-hatchling
+ python-nbconvert
+ python-nbformat
+ python-parameterized
+ python-pytest))
+ (propagated-inputs (list python-numpy))
+ (home-page "https://einops.rocks/")
+ (synopsis "Tensor operations for different backends")
+ (description "Einops provides a set of tensor operations for NumPy and
+multiple deep learning frameworks.")
+ (license license:expat)))
+
(define-public python-xarray
(package
(name "python-xarray")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:03 GMT) Full text and rfc822 format available.Message #17 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 4/9] gnu: python-xarray: Update to 2023.5.0. Date: Sat, 20 May 2023 23:12:36 +0000
* gnu/packages/python-science.scm (python-xarray): Update to 2023.5.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Don't override the check phase.
---
gnu/packages/python-science.scm | 14 ++++----------
1 file changed, 4 insertions(+), 10 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 91c3904783..468da66a2b 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -9,7 +9,7 @@
;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul <at> autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois <at> gmx.com>
-;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego <at> posteo.net>
;;; Copyright © 2021 Greg Hogan <code <at> greghogan.com>
;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
@@ -706,24 +706,18 @@ (define-public python-einops
(define-public python-xarray
(package
(name "python-xarray")
- (version "0.15.1")
+ (version "2023.5.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "xarray" version))
(sha256
(base32
- "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
- (build-system python-build-system)
+ "1s05ykxbhid8q0wbdns3kksdbbmxv47asmqwgp5wxfc284gnb2ii"))))
+ (build-system pyproject-build-system)
(native-inputs
(list python-setuptools-scm python-pytest))
(propagated-inputs
(list python-numpy python-pandas))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "pytest"))))))
(home-page "https://github.com/pydata/xarray")
(synopsis "N-D labeled arrays and datasets")
(description "Xarray (formerly xray) makes working with labelled
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:04 GMT) Full text and rfc822 format available.Message #20 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 5/9] gnu: Add python-xarray-einstats. Date: Sat, 20 May 2023 23:12:37 +0000
* gnu/packages/python-science.scm (python-xarray-einstats): New variable.
---
gnu/packages/python-science.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 468da66a2b..d076c877fc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -730,6 +730,30 @@ (define-public python-xarray
and visualization with these data structures.")
(license license:asl2.0)))
+(define-public python-xarray-einstats
+ (package
+ (name "python-xarray-einstats")
+ (version "0.5.1")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/arviz-devs/xarray-einstats")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-einops python-flit-core python-numba
+ python-pytest))
+ (propagated-inputs (list python-numpy python-scipy python-xarray))
+ (home-page "https://einstats.python.arviz.org/en/latest/")
+ (synopsis "Stats, linear algebra and einops for xarray")
+ (description
+ "@code{xarray_einstats} provides wrappers around some NumPy and SciPy
+functions and around einops with an API and features adapted to xarray.")
+ (license license:asl2.0)))
+
(define-public python-msgpack-numpy
(package
(name "python-msgpack-numpy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:04 GMT) Full text and rfc822 format available.Message #23 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 6/9] gnu: Add python-arviz. Date: Sat, 20 May 2023 23:12:38 +0000
* gnu/packages/statistics.scm (python-arviz): New variable.
---
gnu/packages/statistics.scm | 41 +++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 574790731e..c39cf9c0ac 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2151,6 +2151,47 @@ (define-public python-hdmedians
machine learning, computer vision, and high-dimensional statistics.")
(license license:asl2.0)))
+(define-public python-arviz
+ (package
+ (name "python-arviz")
+ (version "0.15.1")
+ (source (origin
+ (method git-fetch) ; PyPI misses some test files
+ (uri (git-reference
+ (url "https://github.com/arviz-devs/arviz")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0nqr4v927r9kc50z7rwlk2m8nw3dnnmmwmwcfijzd93gbg53wc4f"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; FIXME: matplotlib tests fail because of the "--save" test flag.
+ (list #:test-flags #~'("--ignore"
+ "arviz/tests/base_tests/test_plots_matplotlib.py")
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'write-permission
+ (lambda _
+ ;; 3 tests require write permission.
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs (list python-cloudpickle python-pytest))
+ (propagated-inputs (list python-h5netcdf
+ python-matplotlib
+ python-numpy
+ python-packaging
+ python-pandas
+ python-scipy
+ python-typing-extensions
+ python-xarray
+ python-xarray-einstats))
+ (home-page "https://github.com/arviz-devs/arviz")
+ (synopsis "Exploratory analysis of Bayesian models")
+ (description
+ "ArviZ is a Python package for exploratory analysis of Bayesian models.
+It includes functions for posterior analysis, data storage, model checking,
+comparison and diagnostics.")
+ (license license:asl2.0)))
+
(define-public python-patsy
(package
(name "python-patsy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:14:04 GMT) Full text and rfc822 format available.Message #26 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 7/9] gnu: Add python-fastprogress. Date: Sat, 20 May 2023 23:12:39 +0000
* gnu/packages/python-xyz.scm (python-fastprogress): New variable.
---
gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f061fb4cfd..9ee45ab525 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3002,6 +3002,32 @@ (define-public python-capturer
for additional processing.")
(license license:expat)))
+(define-public python-fastprogress
+ (package
+ (name "python-fastprogress")
+ (version "1.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastai/fastprogress")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "01h8f786wgmmd3fj98wk1n5id67nsp19gs8bbgims04aciwhvj21"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f ;there are no tests
+ #:phases #~(modify-phases %standard-phases
+ ;; XXX: Fails with: "In procedure utime: No such file
+ ;; or directory".
+ (delete 'ensure-no-mtimes-pre-1980))))
+ (home-page "https://github.com/fastai/fastprogress")
+ (synopsis "Progress bar for Jupyter Notebook and console")
+ (description
+ "Fastprogress is a progress bar for Jupyter Notebook and console.")
+ (license license:asl2.0)))
+
(define-public python-case
(package
(name "python-case")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:15:02 GMT) Full text and rfc822 format available.Message #29 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 8/9] gnu: Add python-pytensor. Date: Sat, 20 May 2023 23:12:40 +0000
* gnu/packages/python-science.scm (python-pytensor): New variable.
---
gnu/packages/python-science.scm | 78 +++++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d076c877fc..a419f4d023 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -754,6 +754,84 @@ (define-public python-xarray-einstats
functions and around einops with an API and features adapted to xarray.")
(license license:asl2.0)))
+(define-public python-pytensor
+ (package
+ (name "python-pytensor")
+ (version "2.11.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pymc-devs/pytensor")
+ (commit (string-append "rel-" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1qg38jv1244v5lzjgnb116jpz1gj8p3c5pjxr2nvkx7qpjwzxvk6"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'write-permissions
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ (add-after 'unpack 'versioneer
+ (lambda _
+ ;; Our version of versioneer needs setup.cfg.
+ ;; This is adapted from pyproject.toml.
+ (with-output-to-file "setup.cfg"
+ (lambda ()
+ (display
+ "[versioneer]
+VCS = git
+style = pep440
+versionfile_source = pytensor/_version.py
+versionfile_build = pytensor/_version.py
+tag_prefix = rel-
+")))
+ (invoke "versioneer" "install")
+ (substitute* "setup.py"
+ (("versioneer.get_version\\(\\)")
+ (string-append "\""
+ #$version "\"")))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Test discovery fails, have to call pytest by hand
+ ;; test_tensor_basic.py file requires JAX.
+ (invoke "python" "-m" "pytest" "-vv"
+ "--ignore"
+ "tests/link/jax/test_tensor_basic.py"
+ ;; Skip benchmark tests.
+ "-k"
+ (string-append "not test_elemwise_speed"
+ " and not test_logsumexp_benchmark"
+ " and not test_fused_elemwise_benchmark"
+ " and not test_scan_multiple_output"
+ " and not test_vector_taps_benchmark"
+ " and not test_cython_performance")
+ ;; Skip computationally intensive tests.
+ "--ignore" "tests/scan/"
+ "--ignore" "tests/tensor/"
+ "--ignore" "tests/sandbox/"
+ "--ignore" "tests/sparse/sandbox/")))))))
+ (native-inputs (list python-cython python-pytest python-versioneer))
+ (propagated-inputs (list python-cons
+ python-etuples
+ python-filelock
+ python-logical-unification
+ python-minikanren
+ python-numba
+ python-numpy
+ python-scipy
+ python-typing-extensions))
+ (home-page "https://pytensor.readthedocs.io/en/latest/")
+ (synopsis
+ "Library for mathematical expressions in multi-dimensional arrays")
+ (description
+ "PyTensor is a Python library that allows one to define,
+optimize, and efficiently evaluate mathematical expressions involving
+multi-dimensional arrays. It is a fork of the Aesara library.")
+ (license license:bsd-3)))
+
(define-public python-msgpack-numpy
(package
(name "python-msgpack-numpy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Sat, 20 May 2023 23:15:02 GMT) Full text and rfc822 format available.Message #32 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH 9/9] gnu: Add python-pymc. Date: Sat, 20 May 2023 23:12:41 +0000
* gnu/packages/statistics.scm (python-pymc): New variable.
---
gnu/packages/statistics.scm | 40 +++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c39cf9c0ac..4aac3369ad 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2192,6 +2192,46 @@ (define-public python-arviz
comparison and diagnostics.")
(license license:asl2.0)))
+(define-public python-pymc
+ (package
+ (name "python-pymc")
+ (version "5.3.1")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/pymc-devs/pymc")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1295b0d1zgnpy2hgm0i9jhnnqgzkya7cwcyhq45fdrz65mi9b65h"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; Tests are computationally intensive and around 130 tests out of ~2800
+ ;; fail due to a missing .cc file in PyTensor.
+ (list #:tests? #f
+ #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'write-permissions
+ (lambda _
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs (list python-pytest-cov))
+ (propagated-inputs (list python-arviz
+ python-cachetools
+ python-cloudpickle
+ python-fastprogress
+ python-numpy
+ python-pandas
+ python-pytensor
+ python-scipy
+ python-typing-extensions))
+ (home-page "https://github.com/pymc-devs/pymc")
+ (synopsis "Library for probabilistic programming in Python")
+ (description
+ "PyMC (formerly PyMC3) is a Python package for Bayesian
+statistical modeling focusing on advanced Markov chain Monte Carlo (MCMC) and
+variational inference (VI) algorithms.")
+ (license license:asl2.0)))
+
(define-public python-patsy
(package
(name "python-patsy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Mon, 05 Jun 2023 13:03:02 GMT) Full text and rfc822 format available.Message #35 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: Vinicius Monego <monego <at> posteo.net> Cc: 63619 <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Mon, 05 Jun 2023 15:01:55 +0200
Vinicius Monego <monego <at> posteo.net> skribis: > This patchset adds the PyMC probabilistic programming package. > > Vinicius Monego (9): > gnu: Add python-vega-datasets. > gnu: Add python-altair. > gnu: Add python-einops. > gnu: python-xarray: Update to 2023.5.0. > gnu: Add python-xarray-einstats. > gnu: Add python-arviz. > gnu: Add python-fastprogress. > gnu: Add python-pytensor. > gnu: Add python-pymc. Hi! From a quick glance it LGTM. <https://qa.guix.gnu.org/issue/63619> is still lagging behind though. Ludo’.
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:01 GMT) Full text and rfc822 format available.Message #38 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 1/9] gnu: Add python-vega-datasets. Date: Fri, 9 Jun 2023 03:49:33 +0000
* gnu/packages/statistics.scm (python-vega-datasets): New variable.
---
gnu/packages/statistics.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 42ee83d161..7f6dae1d67 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2062,6 +2062,26 @@ (define-public r-xtable
"This package provides tools to export R data as LaTeX and HTML tables.")
(license license:gpl2+)))
+(define-public python-vega-datasets
+ (package
+ (name "python-vega-datasets")
+ (version "0.9.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "vega_datasets" version))
+ (sha256
+ (base32
+ "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ `(#:tests? #f)) ; this is a data-only package, so no tests
+ (propagated-inputs (list python-pandas))
+ (home-page "https://github.com/altair-viz/vega_datasets")
+ (synopsis "Example datasets used by Vega-related projects")
+ (description "This package provides a collection of datasets used in Vega
+and Vega-Lite examples.")
+ (license license:expat)))
+
(define-public python-hdmedians
(package
(name "python-hdmedians")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:02 GMT) Full text and rfc822 format available.Message #41 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 2/9] gnu: Add python-altair. Date: Fri, 9 Jun 2023 03:49:34 +0000
* gnu/packages/statistics.scm (python-altair): New variable.
---
gnu/packages/statistics.scm | 40 +++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7f6dae1d67..4952e16384 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -85,6 +85,7 @@ (define-module (gnu packages statistics)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
@@ -2082,6 +2083,45 @@ (define-public python-vega-datasets
and Vega-Lite examples.")
(license license:expat)))
+(define-public python-altair
+ (package
+ (name "python-altair")
+ (version "5.0.1")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/altair-viz/altair")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1r74v5n51br9pjhxdzrr62cdgnwkapci93aifnl8dqmfpizfpd7d"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; First two open an external connection.
+ ;; Last introduces a circular dependency on altair-viewer.
+ (list #:test-flags #~(list "-k" (string-append
+ "not test_from_and_to_json_roundtrip"
+ " and not test_render_examples_to_chart"
+ " and not test_save_html"))))
+ (propagated-inputs (list python-jinja2
+ python-jsonschema
+ python-numpy
+ python-pandas
+ python-toolz
+ python-typing-extensions))
+ (native-inputs (list python-black
+ python-hatchling
+ python-ipython
+ python-m2r
+ python-pytest
+ python-vega-datasets))
+ (home-page "https://altair-viz.github.io/")
+ (synopsis "Declarative statistical visualization library for Python")
+ (description
+ "Vega-Altair is a declarative statistical visualization library for Python.")
+ (license license:expat)))
+
(define-public python-hdmedians
(package
(name "python-hdmedians")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:02 GMT) Full text and rfc822 format available.Message #44 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 3/9] gnu: Add python-einops. Date: Fri, 9 Jun 2023 03:49:35 +0000
* gnu/packages/python-science.scm (python-einops): New variable.
---
gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7d3319e367..91c3904783 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -669,6 +669,40 @@ (define-public python-geosketch
necessary for reproducing the experiments in the paper.")
(license license:expat)))
+(define-public python-einops
+ (package
+ (name "python-einops")
+ (version "0.6.1")
+ (source (origin
+ (method git-fetch) ;PyPI misses .ipynb files required for tests
+ (uri (git-reference
+ (url "https://github.com/arogozhnikov/einops")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1h8p39kd7ylg99mh620xr20hg7v78x1jnj6vxwk31rlw2dmv2dpr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-backend
+ (lambda _
+ ;; Einops supports different backends, but we test
+ ;; only NumPy for availability and simplicity.
+ (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
+ (native-inputs (list jupyter
+ python-hatchling
+ python-nbconvert
+ python-nbformat
+ python-parameterized
+ python-pytest))
+ (propagated-inputs (list python-numpy))
+ (home-page "https://einops.rocks/")
+ (synopsis "Tensor operations for different backends")
+ (description "Einops provides a set of tensor operations for NumPy and
+multiple deep learning frameworks.")
+ (license license:expat)))
+
(define-public python-xarray
(package
(name "python-xarray")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:03 GMT) Full text and rfc822 format available.Message #47 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 4/9] gnu: python-xarray: Update to 2023.5.0. Date: Fri, 9 Jun 2023 03:49:36 +0000
* gnu/packages/python-science.scm (python-xarray): Update to 2023.5.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Don't override the check phase.
---
gnu/packages/python-science.scm | 14 ++++----------
1 file changed, 4 insertions(+), 10 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 91c3904783..468da66a2b 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -9,7 +9,7 @@
;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul <at> autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois <at> gmx.com>
-;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego <at> posteo.net>
;;; Copyright © 2021 Greg Hogan <code <at> greghogan.com>
;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
@@ -706,24 +706,18 @@ (define-public python-einops
(define-public python-xarray
(package
(name "python-xarray")
- (version "0.15.1")
+ (version "2023.5.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "xarray" version))
(sha256
(base32
- "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
- (build-system python-build-system)
+ "1s05ykxbhid8q0wbdns3kksdbbmxv47asmqwgp5wxfc284gnb2ii"))))
+ (build-system pyproject-build-system)
(native-inputs
(list python-setuptools-scm python-pytest))
(propagated-inputs
(list python-numpy python-pandas))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "pytest"))))))
(home-page "https://github.com/pydata/xarray")
(synopsis "N-D labeled arrays and datasets")
(description "Xarray (formerly xray) makes working with labelled
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:03 GMT) Full text and rfc822 format available.Message #50 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 5/9] gnu: Add python-xarray-einstats. Date: Fri, 9 Jun 2023 03:49:37 +0000
* gnu/packages/python-science.scm (python-xarray-einstats): New variable.
---
gnu/packages/python-science.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 468da66a2b..d076c877fc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -730,6 +730,30 @@ (define-public python-xarray
and visualization with these data structures.")
(license license:asl2.0)))
+(define-public python-xarray-einstats
+ (package
+ (name "python-xarray-einstats")
+ (version "0.5.1")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/arviz-devs/xarray-einstats")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-einops python-flit-core python-numba
+ python-pytest))
+ (propagated-inputs (list python-numpy python-scipy python-xarray))
+ (home-page "https://einstats.python.arviz.org/en/latest/")
+ (synopsis "Stats, linear algebra and einops for xarray")
+ (description
+ "@code{xarray_einstats} provides wrappers around some NumPy and SciPy
+functions and around einops with an API and features adapted to xarray.")
+ (license license:asl2.0)))
+
(define-public python-msgpack-numpy
(package
(name "python-msgpack-numpy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:04 GMT) Full text and rfc822 format available.Message #53 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 6/9] gnu: Add python-arviz. Date: Fri, 9 Jun 2023 03:49:38 +0000
* gnu/packages/statistics.scm (python-arviz): New variable.
---
gnu/packages/statistics.scm | 41 +++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4952e16384..0a2ca7ced2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2152,6 +2152,47 @@ (define-public python-hdmedians
machine learning, computer vision, and high-dimensional statistics.")
(license license:asl2.0)))
+(define-public python-arviz
+ (package
+ (name "python-arviz")
+ (version "0.15.1")
+ (source (origin
+ (method git-fetch) ; PyPI misses some test files
+ (uri (git-reference
+ (url "https://github.com/arviz-devs/arviz")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0nqr4v927r9kc50z7rwlk2m8nw3dnnmmwmwcfijzd93gbg53wc4f"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; FIXME: matplotlib tests fail because of the "--save" test flag.
+ (list #:test-flags #~'("--ignore"
+ "arviz/tests/base_tests/test_plots_matplotlib.py")
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'write-permission
+ (lambda _
+ ;; 3 tests require write permission.
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs (list python-cloudpickle python-pytest))
+ (propagated-inputs (list python-h5netcdf
+ python-matplotlib
+ python-numpy
+ python-packaging
+ python-pandas
+ python-scipy
+ python-typing-extensions
+ python-xarray
+ python-xarray-einstats))
+ (home-page "https://github.com/arviz-devs/arviz")
+ (synopsis "Exploratory analysis of Bayesian models")
+ (description
+ "ArviZ is a Python package for exploratory analysis of Bayesian models.
+It includes functions for posterior analysis, data storage, model checking,
+comparison and diagnostics.")
+ (license license:asl2.0)))
+
(define-public python-patsy
(package
(name "python-patsy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:04 GMT) Full text and rfc822 format available.Message #56 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 7/9] gnu: Add python-fastprogress. Date: Fri, 9 Jun 2023 03:49:39 +0000
* gnu/packages/python-xyz.scm (python-fastprogress): New variable.
---
gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index efac1130a9..7798bf20ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3041,6 +3041,32 @@ (define-public python-capturer
for additional processing.")
(license license:expat)))
+(define-public python-fastprogress
+ (package
+ (name "python-fastprogress")
+ (version "1.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastai/fastprogress")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "01h8f786wgmmd3fj98wk1n5id67nsp19gs8bbgims04aciwhvj21"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f ;there are no tests
+ #:phases #~(modify-phases %standard-phases
+ ;; XXX: Fails with: "In procedure utime: No such file
+ ;; or directory".
+ (delete 'ensure-no-mtimes-pre-1980))))
+ (home-page "https://github.com/fastai/fastprogress")
+ (synopsis "Progress bar for Jupyter Notebook and console")
+ (description
+ "Fastprogress is a progress bar for Jupyter Notebook and console.")
+ (license license:asl2.0)))
+
(define-public python-case
(package
(name "python-case")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:51:04 GMT) Full text and rfc822 format available.Message #59 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 8/9] gnu: Add python-pytensor. Date: Fri, 9 Jun 2023 03:49:40 +0000
* gnu/packages/python-science.scm (python-pytensor): New variable.
---
gnu/packages/python-science.scm | 76 +++++++++++++++++++++++++++++++++
1 file changed, 76 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d076c877fc..fb2ea0c3b5 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -754,6 +754,82 @@ (define-public python-xarray-einstats
functions and around einops with an API and features adapted to xarray.")
(license license:asl2.0)))
+(define-public python-pytensor
+ (package
+ (name "python-pytensor")
+ (version "2.12.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pymc-devs/pytensor")
+ (commit (string-append "rel-" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1yrzc6idbpvxs7xfmrpbnawz854yq73l7nc6yxdyg0l273ip3jsz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Replace version manually because pytensor uses
+ ;; versioneer, which requires git metadata.
+ (add-after 'unpack 'versioneer
+ (lambda _
+ (with-output-to-file "setup.cfg"
+ (lambda ()
+ (display "\
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = pytensor/_version.py
+versionfile_build = pytensor/_version.py
+tag_prefix =
+parentdir_prefix = pytensor-
+")))
+ (invoke "versioneer" "install")
+ (substitute* "setup.py"
+ (("versioneer.get_version\\(\\)")
+ (string-append "\"" #$version "\"")))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Test discovery fails, have to call pytest by hand.
+ ;; test_tensor_basic.py file requires JAX.
+ (invoke "python" "-m" "pytest" "-vv"
+ "--ignore" "tests/link/jax/test_tensor_basic.py"
+ ;; Skip benchmark tests.
+ "-k" (string-append
+ "not test_elemwise_speed"
+ " and not test_logsumexp_benchmark"
+ " and not test_fused_elemwise_benchmark"
+ " and not test_scan_multiple_output"
+ " and not test_vector_taps_benchmark"
+ " and not test_cython_performance")
+ ;; Skip computationally intensive tests.
+ "--ignore" "tests/scan/"
+ "--ignore" "tests/tensor/"
+ "--ignore" "tests/sandbox/"
+ "--ignore" "tests/sparse/sandbox/")))))))
+ (native-inputs (list python-cython python-pytest python-versioneer))
+ (propagated-inputs (list python-cons
+ python-etuples
+ python-filelock
+ python-logical-unification
+ python-minikanren
+ python-numba
+ python-numpy
+ python-scipy
+ python-typing-extensions))
+ (home-page "https://pytensor.readthedocs.io/en/latest/")
+ (synopsis
+ "Library for mathematical expressions in multi-dimensional arrays")
+ (description
+ "PyTensor is a Python library that allows one to define,
+optimize, and efficiently evaluate mathematical expressions involving
+multi-dimensional arrays. It is a fork of the Aesara library.")
+ (license license:bsd-3)))
+
(define-public python-msgpack-numpy
(package
(name "python-msgpack-numpy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 03:52:02 GMT) Full text and rfc822 format available.Message #62 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 63619 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v2 9/9] gnu: Add python-pymc. Date: Fri, 9 Jun 2023 03:49:41 +0000
* gnu/packages/statistics.scm (python-pymc): New variable.
---
gnu/packages/statistics.scm | 57 +++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0a2ca7ced2..c2dbfbb64a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2193,6 +2193,63 @@ (define-public python-arviz
comparison and diagnostics.")
(license license:asl2.0)))
+(define-public python-pymc
+ (package
+ (name "python-pymc")
+ (version "5.4.1")
+ (source (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/pymc-devs/pymc")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ihx4r7z2lllcakl63dfgskhyk6kns5qp6fi1xf9bhzdy1wbwfls"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f ; tests are too computationally intensive
+ #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'versioneer
+ (lambda _
+ (with-output-to-file "setup.cfg"
+ (lambda ()
+ (display "\
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = pymc/_version.py
+versionfile_build = pymc/_version.py
+tag_prefix =
+parentdir_prefix = pymc-
+")))
+ (invoke "versioneer" "install")
+ (substitute* "setup.py"
+ (("versioneer.get_version\\(\\)")
+ (string-append "\"" #$version "\"")))))
+ ;; To create the compiledir for tests.
+ (add-before 'check 'write-permissions
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")))))))
+ (native-inputs (list python-pytest-cov python-versioneer))
+ (propagated-inputs (list python-arviz
+ python-cachetools
+ python-cloudpickle
+ python-fastprogress
+ python-numpy
+ python-pandas
+ python-pytensor
+ python-scipy
+ python-typing-extensions))
+ (home-page "https://github.com/pymc-devs/pymc")
+ (synopsis "Library for probabilistic programming in Python")
+ (description
+ "PyMC (formerly PyMC3) is a Python package for Bayesian
+statistical modeling focusing on advanced Markov chain Monte Carlo (MCMC) and
+variational inference (VI) algorithms.")
+ (license license:asl2.0)))
+
(define-public python-patsy
(package
(name "python-patsy")
--
2.34.1
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Fri, 09 Jun 2023 04:11:01 GMT) Full text and rfc822 format available.Message #65 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: Ludovic Courtès <ludo <at> gnu.org> Cc: 63619 <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Fri, 09 Jun 2023 04:10:16 +0000
Em seg, 2023-06-05 às 15:01 +0200, Ludovic Courtès escreveu: [...] > Hi! From a quick glance it LGTM. > > <https://qa.guix.gnu.org/issue/63619> is still lagging behind though. > > Ludo’. Hi, I finally understood Versioneer, and fixed the version reporting in pytensor and pymc. I also updated some of the packages and now pytensor correctly installs "Faddeeva.h". My last question would be about the python-vega-datasets package. The dataset licenses must be "MIT compatible", I'm not sure whether that implies FSDG compatibility. Some of them do not mention the license: https://github.com/altair-viz/vega_datasets/blob/master/vega_datasets/dataset_info.json Developer acknowledges that the provenance of the datasets is difficult to trace: https://github.com/altair-viz/vega_datasets/issues/1#issue-288302709 If it's not a problem, then I can push it soon. And I just noticed that there are tests in this package, they will be enabled before pushing.
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Wed, 14 Jun 2023 21:06:02 GMT) Full text and rfc822 format available.Message #68 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: Vinicius Monego <monego <at> posteo.net> Cc: 63619 <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Wed, 14 Jun 2023 23:05:14 +0200
Hi, Vinicius Monego <monego <at> posteo.net> skribis: > My last question would be about the python-vega-datasets package. The > dataset licenses must be "MIT compatible", I'm not sure whether that > implies FSDG compatibility. Some of them do not mention the license: > > https://github.com/altair-viz/vega_datasets/blob/master/vega_datasets/dataset_info.json > > Developer acknowledges that the provenance of the datasets is difficult > to trace: > https://github.com/altair-viz/vega_datasets/issues/1#issue-288302709 > > If it's not a problem, then I can push it soon. And I just noticed that > there are tests in this package, they will be enabled before pushing. Lack of licensing and provenance information is usually not a good sign. What did Debian do, for example? Note that FSDG is more lax than Debian when it comes to “Non-functional data”¹. Thanks, Ludo’. ¹ https://www.gnu.org/distros/free-system-distribution-guidelines.html
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Wed, 14 Jun 2023 22:48:02 GMT) Full text and rfc822 format available.Message #71 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: Ludovic Courtès <ludo <at> gnu.org> Cc: 63619 <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Wed, 14 Jun 2023 22:46:45 +0000
Em qua, 2023-06-14 às 23:05 +0200, Ludovic Courtès escreveu: [...] > Lack of licensing and provenance information is usually not a good > sign. What did Debian do, for example? > > Note that FSDG is more lax than Debian when it comes to “Non- > functional > data”¹. > > Thanks, > Ludo’. > > ¹ > https://www.gnu.org/distros/free-system-distribution-guidelines.html Debian has a patch to remove the "L.A. Riots" dataset with the following justification: > vega_datasets/_data/la-riots.csv is removed since the license is not > clear and the file is not currently available from Los Angeles Times > for European users. So they don't seem to have a problem with the licenses of the other datasets. Vinicius
guix-patches <at> gnu.org:bug#63619; Package guix-patches.
(Wed, 21 Jun 2023 21:49:02 GMT) Full text and rfc822 format available.Message #74 received at 63619 <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: Vinicius Monego <monego <at> posteo.net> Cc: 63619 <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Wed, 21 Jun 2023 23:48:06 +0200
Hi, Vinicius Monego <monego <at> posteo.net> skribis: > Debian has a patch to remove the "L.A. Riots" dataset with the > following justification: > >> vega_datasets/_data/la-riots.csv is removed since the license is not >> clear and the file is not currently available from Los Angeles Times >> for European users. > > So they don't seem to have a problem with the licenses of the other > datasets. OK, good to know. So I’d say you can keep them, adding links to the relevant discussions for future reference. Thanks, Ludo’.
Vinicius Monego <monego <at> posteo.net>:Vinicius Monego <monego <at> posteo.net>:Message #79 received at 63619-done <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: Ludovic Courtès <ludo <at> gnu.org> Cc: 63619-done <at> debbugs.gnu.org Subject: Re: bug#63619: [PATCH 0/9] Add PyMC. Date: Sun, 25 Jun 2023 14:01:34 +0000
Em qua, 2023-06-21 às 23:48 +0200, Ludovic Courtès escreveu: > Hi, > > Vinicius Monego <monego <at> posteo.net> skribis: > > > Debian has a patch to remove the "L.A. Riots" dataset with the > > following justification: > > > > > vega_datasets/_data/la-riots.csv is removed since the license is > > > not > > > clear and the file is not currently available from Los Angeles > > > Times > > > for European users. > > > > So they don't seem to have a problem with the licenses of the other > > datasets. > > OK, good to know. So I’d say you can keep them, adding links to the > relevant discussions for future reference. > > Thanks, > Ludo’. Thanks for the review. Applied with the patch imported from Debian. Vinicius
Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Mon, 24 Jul 2023 11:24:04 GMT) Full text and rfc822 format available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.