[bug#38652] (no subject)

[bug#38652] (no subject)

[mpatras]

-- 
Mădălin Ionel Patrașcu

System Administrator
Bioinformatics and Omics Data Science
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Hannoversche Str. 28, 10115 Berlin
House 101, room 1.60

[bug#38652] [PATCH 1/5] gnu: python-dill: Update to 0.3.1.1.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-dill): Update to 0.3.1.1.
---
 gnu/packages/python-xyz.scm | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f0490f248c..9075dfeb49 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15651,17 +15651,25 @@ object-oriented library such as @code{scikit-learn}.")
 (define-public python-dill
   (package
     (name "python-dill")
-    (version "0.2.9")
+    (version "0.3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dill" version))
        (sha256
-        (base32 "0vwqyi6hyz2r29zydc78dqymkbc5y7gia16xcdh215cikxph9mpn"))))
+        (base32 "1704g8z70d210ksgbccs2v545v9w0wc6lx15m296alb7jf0yzn22"))))
     (build-system python-build-system)
-    ;; FIXME: The check phase fails with "don't know how to make test from: …".
-    (arguments '(#:tests? #f))
-    (home-page "https://pypi.org/project/dill")
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (with-directory-excursion "/tmp"
+               (invoke "nosetests" "-v"))
+             #t)))))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://pypi.org/project/dill/")
     (synopsis "Serialize all of Python")
     (description "Dill extends Python's @code{pickle} module for serializing
 and de-serializing Python objects to the majority of the built-in Python
-- 
2.24.1

[bug#38652] [PATCH 2/5] gnu: python-multiprocess: Update to 0.70.9.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-multiprocess): Update to 0.70.9.
---
 gnu/packages/python-xyz.scm | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9075dfeb49..acc030fb9b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15685,18 +15685,28 @@ the saved state of the original interpreter session.")
 (define-public python-multiprocess
   (package
     (name "python-multiprocess")
-    (version "0.70.6.1")
+    (version "0.70.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiprocess" version))
        (sha256
         (base32
-         "1ip5caz67b3q0553mr8gm8xwsb8x500jn8ml0gihgyfy52m2ypcq"))))
+         "1r882nvd44xqwbrclwqx5rhs80l6809rcvpc7pkpgnij06cvvmcz"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (with-directory-excursion "/tmp"
+               (invoke "nosetests" "-v"))
+             #t)))))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
     (propagated-inputs
      `(("python-dill" ,python-dill)))
-    (home-page "https://pypi.org/project/multiprocess")
+    (home-page "https://pypi.org/project/multiprocess/")
     (synopsis "Multiprocessing and multithreading in Python")
     (description
      "This package is a fork of the multiprocessing Python package, a package
-- 
2.24.1

[bug#38652] [PATCH 3/5] gnu: Add python-ppft.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-ppft): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index acc030fb9b..f5b2ff16e7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16899,3 +16899,38 @@ always possible to declare a command with the highest possible (and least
 flexible) layer and then tune the behaviour with any of the lower layers
 including the native API of @code{python-argparse}.")
       (license license:lgpl3+))))
+
+(define-public python-ppft
+  (package
+    (name "python-ppft")
+    (version "1.6.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ppft" version))
+       (sha256
+        (base32
+         "1z1invkhszc5d2mvgr221v7cszzifcc77mz0pv3wjp6x5q2768cy"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (with-directory-excursion "/tmp"
+               (invoke "nosetests" "-v"))
+             #t)))))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (propagated-inputs
+     `(("python-six" ,python-six)))
+    (home-page "https://pypi.org/project/ppft/")
+    (synopsis "Fork of Parallel Python")
+    (description
+     "This package phython-ppft is a fork of Parallel Python, and is developed
+as part of python-pathos.  Parallel Python module (pp) provides an easy and
+efficient way to create parallel-enabled applications for SMP (symmetric
+multiprocessing) computers and clusters.  pp module features cross-platform
+portability and dynamic load balancing.")
+    ;; looks like bsd-3 https://github.com/uqfoundation/ppft/blob/master/LICENSE
+    (license license:bsd-3)))
-- 
2.24.1

[bug#38652] [PATCH 4/5] gnu: Add python-pox.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-pox): 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 f5b2ff16e7..2287903d0b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16934,3 +16934,27 @@ multiprocessing) computers and clusters.  pp module features cross-platform
 portability and dynamic load balancing.")
     ;; looks like bsd-3 https://github.com/uqfoundation/ppft/blob/master/LICENSE
     (license license:bsd-3)))
+
+(define-public python-pox
+  (package
+    (name "python-pox")
+    (version "0.2.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pox" version))
+       (sha256
+        (base32
+         "0y17ckc2p6i6709s279sjdj4q459mpcc38ymg9zv9y6vl6jf3bq6"))))
+    (build-system python-build-system)
+    (home-page "https://pypi.org/project/pox/")
+    (synopsis "Python utilities for filesystem exploration and automated builds")
+    (description
+     "Python-pox provides a collection of utilities for navigating and
+manipulating filesystems.  This module is designed to facilitate some of the
+low level operating system interactions that are useful when exploring a
+filesystem on a remote host.  Python-pox provides python equivalents of several
+unix shell commands such as which and find.  These commands allow automated
+discovery of what has been installed on an operating system, and where the
+essential tools are located.")
+    (license license:bsd-3)))
-- 
2.24.1

[bug#38652] [PATCH 5/5] gnu: Add python-pathos.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-pathos, python2-pathos): New variables.
---
 gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2287903d0b..edaefe7575 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16958,3 +16958,34 @@ unix shell commands such as which and find.  These commands allow automated
 discovery of what has been installed on an operating system, and where the
 essential tools are located.")
     (license license:bsd-3)))
+
+(define-public python-pathos
+  (package
+    (name "python-pathos")
+    (version "0.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pathos" version))
+       (sha256
+        (base32
+         "0in8hxdz7k081ijn6q94gr39ycy7363sx4zysmbwyvd7snqjrbi1"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-dill" ,python-dill)
+       ("python-multiprocess" ,python-multiprocess)
+       ("python-pox" ,python-pox)
+       ("python-ppft" ,python-ppft)))
+    (home-page "https://pypi.org/project/pathos/")
+    (synopsis
+     "Parallel graph management and execution in heterogeneous computing")
+    (description
+     "Python-pathos is a framework for heterogenous computing.  It provides a
+consistent high-level interface for configuring and launching parallel
+computations across heterogenous resources.  Python-pathos provides configurable
+launchers for parallel and distributed computing, where each launcher contains
+the syntactic logic to configure and launch jobs in an execution environment.")
+    (license license:bsd-3)))
+
+(define-public python2-pathos
+  (package-with-python2 python-pathos))
-- 
2.24.1

[bug#38652] [PATCH 3/5] gnu: Add python-ppft.

[Ricardo Wurmus]

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-ppft): New variable.
[…]
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (replace 'check
> +           (lambda _
> +             (with-directory-excursion "/tmp"
> +               (invoke "nosetests" "-v"))
> +             #t)))))

This has the effect of not running the tests at all.

-- 
Ricardo

[bug#38652] [PATCH 5/5] gnu: Add python-pathos.

[Ricardo Wurmus]

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-pathos, python2-pathos): New variables.

I can’t seem to get the tests to run.  I tried this:

--8<---------------cut here---------------start------------->8---
(define-public python-pathos
  (package
    (name "python-pathos")
    (version "0.2.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pathos" version))
       (sha256
        (base32
         "0in8hxdz7k081ijn6q94gr39ycy7363sx4zysmbwyvd7snqjrbi1"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "py.test" "-vvv" "tests")
             #t)))))
    (propagated-inputs
     `(("python-dill" ,python-dill)
       ("python-multiprocess" ,python-multiprocess)
       ("python-pox" ,python-pox)
       ("python-ppft" ,python-ppft)))
    (native-inputs
     `(("python-pytest" ,python-pytest)))
    (home-page "https://pypi.org/project/pathos/")
    (synopsis "Parallel graph management and execution in heterogeneous computing")
    (description
     "Pathos is a framework for heterogenous computing.  It provides a
consistent high-level interface for configuring and launching parallel
computations across heterogenous resources.  Pathos provides configurable
launchers for parallel and distributed computing, where each launcher contains
the syntactic logic to configure and launch jobs in an execution
environment.")
    (license license:bsd-3)))
--8<---------------cut here---------------end--------------->8---

…but after collecting 15 tests it just hangs, doing nothing.

> +(define-public python2-pathos
> +  (package-with-python2 python-pathos))

If you define a Python 2 variant you should also define Python 2
variants for all its inputs.

-- 
Ricardo

[bug#38652] [PATCH 5/5] gnu: Add python-pathos.

[Efraim Flashner]

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On Tue, Dec 17, 2019 at 06:24:37PM +0100, Mădălin Ionel Patrașcu wrote:
> * gnu/packages/python-xyz.scm (python-pathos, python2-pathos): New variables.
> ---
> +
> +(define-public python2-pathos
> +  (package-with-python2 python-pathos))
> 

With the impending end of life on python2 we're not automatically adding
python2 variants of packages unless they're actually used.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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bug#38652: [PATCH 5/5] gnu: Add python-pathos.

[Efraim Flashner]

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I pushed this patch and managed to get the test suite to run.


-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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Confidentiality cannot be guaranteed on emails sent or received unencrypted

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