[bug#63621] [PATCH 0/6] Add PyTorch-related statistics libraries.

[bug#63621] [PATCH 0/6] Add PyTorch-related statistics libraries.

[Vinicius Monego]

This patchset adds gpytorch, botorch and Ax.

Vinicius Monego (6):
  gnu: Add python-linear-operator.
  gnu: Add python-gpytorch.
  gnu: python-pyro-ppl: Update to 1.8.4.
  gnu: Add python-botorch.
  gnu: Add python-yappi.
  gnu: Add python-ax-platform.

 gnu/packages/machine-learning.scm | 134 +++++++++++++++++++++++++++++-
 gnu/packages/python-xyz.scm       |  24 ++++++
 2 files changed, 156 insertions(+), 2 deletions(-)

-- 
2.34.1

[bug#63621] [PATCH 1/6] gnu: Add python-linear-operator.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-linear-operator): New variable.
---
 gnu/packages/machine-learning.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 694b050e86..de06b4988a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4080,6 +4080,25 @@ (define-public python-pyro-ppl
 inference.")
     (license license:asl2.0)))
 
+(define-public python-linear-operator
+  (package
+    (name "python-linear-operator")
+    (version "0.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "linear_operator" version))
+              (sha256
+               (base32
+                "1ipm154n8cxnl35i8wrx650a60yxyhjpdpdl1mf7ijaqybwcjmvw"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-pytorch python-scipy))
+    (native-inputs (list python-flake8 python-flake8-print python-twine))
+    (home-page "https://github.com/cornellius-gp/linear_operator/")
+    (synopsis "Linear operator implementation")
+    (description "LinearOperator is a PyTorch package for abstracting away the
+linear algebra routines needed for structured matrices (or operators).")
+    (license license:expat)))
+
 (define-public vosk-api
   (let* ((openfst openfst-for-vosk)
          (kaldi kaldi-for-vosk))
-- 
2.34.1

[bug#63621] [PATCH 2/6] gnu: Add python-gpytorch.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-gpytorch): New variable.
---
 gnu/packages/machine-learning.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index de06b4988a..f4b59556bc 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4099,6 +4099,33 @@ (define-public python-linear-operator
 linear algebra routines needed for structured matrices (or operators).")
     (license license:expat)))
 
+(define-public python-gpytorch
+  (package
+    (name "python-gpytorch")
+    (version "1.10")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "gpytorch" version))
+              (sha256
+               (base32
+                "063zzc515xip3d11y21ld47ca3qq0hqs27jgba20l8mzkympijbd"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; This test failed.
+     (list #:test-flags #~'("-k" "not test_deprecated_methods")))
+    (propagated-inputs (list python-linear-operator python-scikit-learn))
+    (native-inputs (list python-coverage
+                         python-flake8
+                         python-flake8-print
+                         python-nbval
+                         python-pytest
+                         python-twine))
+    (home-page "https://gpytorch.ai")
+    (synopsis "Implementation of Gaussian Processes in Pytorch")
+    (description
+     "GPyTorch is a Gaussian process library implemented using PyTorch.")
+    (license license:expat)))
+
 (define-public vosk-api
   (let* ((openfst openfst-for-vosk)
          (kaldi kaldi-for-vosk))
-- 
2.34.1

[bug#63621] [PATCH 3/6] gnu: python-pyro-ppl: Update to 1.8.4.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-pyro-ppl): Update to 1.8.4.
---
 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f4b59556bc..90bfe283a2 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4009,7 +4009,7 @@ (define-public python-pyro-api
 (define-public python-pyro-ppl
   (package
     (name "python-pyro-ppl")
-    (version "1.8.1")
+    (version "1.8.4")
     ;; The sources on pypi don't include tests.
     (source
      (origin
@@ -4019,7 +4019,7 @@ (define-public python-pyro-ppl
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ns20mr8qgjshzbplrfzaz1xhb9ldbgvrj2rzlsxvns2bi1ddyl5"))))
+        (base32 "1h00i847dsggiw9mmvjbi4nacpjbyqi5wjqg5gbfnmzimhdrgp77"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.34.1

[bug#63621] [PATCH 4/6] gnu: Add python-botorch.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-botorch): New variable.
---
 gnu/packages/machine-learning.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 90bfe283a2..1e34e5fd5e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4126,6 +4126,34 @@ (define-public python-gpytorch
      "GPyTorch is a Gaussian process library implemented using PyTorch.")
     (license license:expat)))
 
+(define-public python-botorch
+  (package
+    (name "python-botorch")
+    (version "0.8.5")
+    (source (origin
+              (method git-fetch) ;no tests in PyPI
+              (uri (git-reference
+                    (url "https://github.com/pytorch/botorch")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1xa98xy5wx0mf6fx62lx5cy84svi695iwcg4n74z4f9wz60lghsm"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-gpytorch
+                             python-linear-operator
+                             python-multipledispatch
+                             python-pyro-ppl
+                             python-scipy
+                             python-pytorch))
+    (native-inputs (list python-black python-flake8 python-pytest
+                         python-pytest-cov python-sphinx))
+    (home-page "https://botorch.org")
+    (synopsis "Bayesian Optimization in PyTorch")
+    (description
+     "BoTorch is a library for Bayesian Optimization built on PyTorch.")
+    (license license:expat)))
+
 (define-public vosk-api
   (let* ((openfst openfst-for-vosk)
          (kaldi kaldi-for-vosk))
-- 
2.34.1

[bug#63621] [PATCH 5/6] gnu: Add python-yappi.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-yappi): New variable.
---
 gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9ee45ab525..c7a31e40a1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3299,6 +3299,30 @@ (define-public python-openpyxl
 standard.")
     (license license:expat)))
 
+(define-public python-yappi
+  (package
+    (name "python-yappi")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "yappi" version))
+              (sha256
+               (base32
+                "1h3zl60pi57ynb3sw7sg2wcn157jwz992y95bv5kcds3qy7msjsh"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-gevent))
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (replace 'check
+                          (lambda* (#:key tests? #:allow-other-keys)
+                            (when tests?
+                              (invoke "python" "run_tests.py")))))))
+    (home-page "https://github.com/sumerc/yappi")
+    (synopsis "Yet Another Python Profiler")
+    (description "Yappi is a tracing profiler that is multithreading, asyncio
+and gevent aware.")
+    (license license:expat)))
+
 (define-public python-eventlet
   (package
     (name "python-eventlet")
-- 
2.34.1

[bug#63621] [PATCH 6/6] gnu: Add python-ax-platform.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-ax-platform): New variable.
---
 gnu/packages/machine-learning.scm | 56 +++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1e34e5fd5e..384c980478 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4154,6 +4154,62 @@ (define-public python-botorch
      "BoTorch is a library for Bayesian Optimization built on PyTorch.")
     (license license:expat)))
 
+(define-public python-ax-platform
+  (package
+    (name "python-ax-platform")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "ax-platform" version))
+              (sha256
+               (base32
+                "1spyp8wjf0jyh7yf002sl4lc1rwbnzdki9ql9a3nzsyyx602flj8"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Ignore tests for tensorboard and torchx, which we don't have.
+     (list #:test-flags
+           #~(list "--ignore" "ax/metrics/tests/test_tensorboard.py"
+                   "--ignore" "ax/runners/tests/test_torchx.py"
+                   ;; This test tries to download online data.
+                   "-k" "not test_torchvision_encode_decode")
+           ;; Ax checks for typeguard==2.13.3 which is the version we have,
+           ;; but the version report in typeguard is fault and displays 0.0.0.
+           #:phases #~(modify-phases %standard-phases
+                        (delete 'sanity-check))))
+    (propagated-inputs (list python-botorch
+                             python-ipywidgets
+                             python-jinja2
+                             python-pandas
+                             python-plotly
+                             python-scikit-learn
+                             python-scipy
+                             python-typeguard))
+    (native-inputs (list jupyter
+                         python-beautifulsoup4
+                         python-black
+                         python-flake8
+                         python-hypothesis
+                         python-jinja2
+                         python-jupyter-client
+                         python-mypy
+                         python-nbconvert
+                         python-pyfakefs
+                         python-pyre-extensions
+                         python-pytest
+                         python-pytest-cov
+                         python-sqlalchemy
+                         python-torchvision
+                         python-yappi))
+    (home-page "https://ax.dev/")
+    (synopsis "Adaptive Experimentation Platform")
+    (description
+     "Ax is an accessible, general-purpose platform for
+understanding, managing, deploying, and automating adaptive experiments.
+Adaptive experimentation is the machine-learning guided process of
+iteratively exploring a (possibly infinite) parameter space in order to
+identify optimal configurations in a resource-efficient manner.")
+    (license license:expat)))
+
 (define-public vosk-api
   (let* ((openfst openfst-for-vosk)
          (kaldi kaldi-for-vosk))
-- 
2.34.1

[bug#63621] [PATCH 0/6] Add PyTorch-related statistics libraries.

[Ludovic Courtès]

Hi Vinicius,

Vinicius Monego <monego@posteo.net> skribis:

> This patchset adds gpytorch, botorch and Ax.
>
> Vinicius Monego (6):
>   gnu: Add python-linear-operator.
>   gnu: Add python-gpytorch.
>   gnu: python-pyro-ppl: Update to 1.8.4.
>   gnu: Add python-botorch.
>   gnu: Add python-yappi.
>   gnu: Add python-ax-platform.

<https://qa.guix.gnu.org/issue/63621> currently says “Yet to process
revision” (perhaps erroneously) but the patch set LGTM, so if the
dependent of python-pyto-ppl still builds fine, I think you can push.

Thanks,
Ludo’.

[bug#63621] [PATCH 0/6] Add PyTorch-related statistics libraries.

[Ludovic Courtès]

Hi!

Friendly reminder.  :-)

Ludovic Courtès <ludo@gnu.org> skribis:

> Hi Vinicius,
>
> Vinicius Monego <monego@posteo.net> skribis:
>
>> This patchset adds gpytorch, botorch and Ax.
>>
>> Vinicius Monego (6):
>>   gnu: Add python-linear-operator.
>>   gnu: Add python-gpytorch.
>>   gnu: python-pyro-ppl: Update to 1.8.4.
>>   gnu: Add python-botorch.
>>   gnu: Add python-yappi.
>>   gnu: Add python-ax-platform.
>
> <https://qa.guix.gnu.org/issue/63621> currently says “Yet to process
> revision” (perhaps erroneously) but the patch set LGTM, so if the
> dependent of python-pyto-ppl still builds fine, I think you can push.
>
> Thanks,
> Ludo’.

[bug#63621] [PATCH 0/6] Add PyTorch-related statistics libraries.

[Vinicius Monego]

Em seg, 2023-08-21 às 15:03 +0200, Ludovic Courtès escreveu:
> Hi!
> 
> Friendly reminder.  :-)

Hi Ludo,

Could you take another look at https://issues.guix.gnu.org/63980? It
doesn't feel right to delete sanity checks in this series or having to
work around it because of typeguard.

I updated the packages to their latest version and had to introduce a
new package (python-jaxtyping). But now some tests are failing in
gpytorch, so I'm taking a look at that.

Vinicius