[bug#56835] [PATCH 0/2]: gnu: Add pynbody (astronomy)

[bug#56835] [PATCH 0/2]: gnu: Add pynbody (astronomy)

[Sharlatan Hellseher]

Hi Guix team!

This patch series add astrophysical Python library - pynbody.

> ./pre-inst-env guix build python-pynbody python-posix-ipc --rounds=2
/gnu/store/1vml0zln3v1ql300l0qqppp2a7kfd73v-python-posix-ipc-1.0.5
/gnu/store/nbnih0fs6ny6b2ldircjfmb03y5a9cjp-python-pynbody-1.2.3

Sharlatan Hellseher (2):
  gnu: Add posix-ipc
  gnu: Add pynbody

 gnu/packages/astronomy.scm  | 68 +++++++++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm | 32 +++++++++++++++++
 2 files changed, 100 insertions(+)


base-commit: 69eb84094516b56d7784aa1b8809cce0936e173e



-- 
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.

[bug#56835] [PATCH 1/2]: gnu: Add posic-ipc

[Sharlatan Hellseher]

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-- 
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.

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From 8631e7afa40a752fe41cacc29a2a4c358a8a1746 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Fri, 29 Jul 2022 17:50:56 +0100
Subject: [PATCH 1/2] gnu: Add posix-ipc

* gnu/packages/python-xyz.scm: (python-posix-ipc): New variable.
---
 gnu/packages/python-xyz.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ac7c0d6066..732cd2a376 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29590,6 +29590,38 @@ (define-public python-queuelib
 fashion.")
     (license license:bsd-3)))
 
+(define-public python-posix-ipc
+  (package
+    (name "python-posix-ipc")
+    (version "1.0.5")
+    (source
+     (origin
+       ;; The source distributed on PyPI is prebuild.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/osvenskan/posix_ipc")
+             (commit (string-append "rel" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17y4d0pmvp199c5hbs602ailhlh9f9zv89kmpbd8jhyl6rgaxsvs"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'patch-cc-path
+                 (lambda _
+                   (substitute* "prober.py"
+                     (("cmd = .cc")
+                      (string-append "cmd = \"" #$(cc-for-target)))))))))
+    (native-inputs
+     (list python-unittest2))
+    (home-page "http://semanchuk.com/philip/posix_ipc/")
+    (synopsis "POSIX IPC primitives for Python")
+    (description
+     "This package provides POSIX IPC primitives - semaphores, shared memory and
+message queues for Python.")
+    (license license:bsd-3))) ; BSD like Copyright (c) 2018, Philip Semanchuk
+
 (define-public python-itemadapter
   (package
     (name "python-itemadapter")
-- 
2.36.1

[bug#56835] [PATCH 2/2]: gnu: Add pynbody

[Sharlatan Hellseher]

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-- 
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.

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From d245a43520d37e33615d825338d1f55dda36fce2 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Fri, 29 Jul 2022 21:17:50 +0100
Subject: [PATCH 2/2] gnu: Add pynbody

* gnu/packages/astronomy.scm: (python-pynbody): New variable.
---
 gnu/packages/astronomy.scm | 68 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e84eb188ff..3b4ded5728 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1606,6 +1606,74 @@ (define-public python-pyerfa
 functions, so that they can be called with scalar or array inputs.")
     (license license:bsd-3)))
 
+(define-public python-pynbody
+  (package
+    (name "python-pynbody")
+    (version "1.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pynbody" version))
+       (sha256
+        (base32 "1jxwk2s4qz1znvyak2lj7ld01kl1jh87xp81ki7a8dz1gcy93fkx"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'disable-tests-require-testdata
+                 (lambda _
+                   ;; Disable tests which need to download additional 1.0GiB+
+                   ;; of test data archive from
+                   ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
+                   ;;    https://github.com/pynbody/pynbody/blob/ \
+                   ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
+                   ;;    .github/workflows/build-test.yaml#L41
+                   (with-directory-excursion "tests"
+                     (for-each delete-file
+                               '("gravity_test.py"
+                                 "adaptahop_test.py"
+                                 "ahf_halos_test.py"
+                                 "array_test.py"
+                                 "bridge_test.py"
+                                 "family_test.py"
+                                 "partial_tipsy_test.py"
+                                 "snapshot_test.py"
+                                 "test_profile.py"
+                                 "gadget_test.py"
+                                 "gadgethdf_test.py"
+                                 "grafic_test.py"
+                                 "halotools_test.py"
+                                 "nchilada_test.py"
+                                 "ramses_new_ptcl_format_test.py"
+                                 "ramses_test.py"
+                                 "rockstar_test.py"
+                                 "sph_image_test.py"
+                                 "sph_smooth_test.py"
+                                 "subfind_test.py"
+                                 "subfindhdf_gadget4_test.py"
+                                 "tipsy_test.py")))))
+               (replace 'check
+                 (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+                   (when tests?
+                     (add-installed-pythonpath inputs outputs)
+                     (setenv "HOME" "/tmp")
+                     (invoke "pytest" "-vv")))))))
+    (native-inputs
+     (list python-pandas python-pytest))
+    (propagated-inputs
+     (list python-cython
+           python-h5py
+           python-matplotlib
+           python-numpy
+           python-posix-ipc
+           python-scipy))
+    (home-page "https://pynbody.github.io/pynbody/index.html")
+    (synopsis "Light-weight astronomical N-body/SPH analysis for python")
+    (description "@code{Pynbody} is an analysis framework for N-body and hydrodynamic
+astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
+N-Chilada and RAMSES AMR outputs.")
+    (license license:gpl3+)))
+
 (define-public python-sep
   (package
     (name "python-sep")
-- 
2.36.1

bug#56835: [PATCH 0/2]: gnu: Add pynbody (astronomy)

[Efraim Flashner]

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On Fri, Jul 29, 2022 at 09:28:19PM +0100, Sharlatan Hellseher wrote:
> Hi Guix team!
> 
> This patch series add astrophysical Python library - pynbody.
> 
> > ./pre-inst-env guix build python-pynbody python-posix-ipc --rounds=2
> /gnu/store/1vml0zln3v1ql300l0qqppp2a7kfd73v-python-posix-ipc-1.0.5
> /gnu/store/nbnih0fs6ny6b2ldircjfmb03y5a9cjp-python-pynbody-1.2.3
> 
> Sharlatan Hellseher (2):
>   gnu: Add posix-ipc
>   gnu: Add pynbody
> 
>  gnu/packages/astronomy.scm  | 68 +++++++++++++++++++++++++++++++++++++
>  gnu/packages/python-xyz.scm | 32 +++++++++++++++++
>  2 files changed, 100 insertions(+)
> 
> 
> base-commit: 69eb84094516b56d7784aa1b8809cce0936e173e

I moved python-cython from propagated-inputs to native-inputs and pushed
the two patches. Thanks!

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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