[bug#59542] [PATCH 0/5] gnu: Add python-sunpy.

[bug#59542] [PATCH 0/5] gnu: Add python-sunpy.

[Sharlatan Hellseher]

Hi Guix team!

This is the last set of patches which adding with SunPy - solar data analysis
environment for Python.

python-opencv is required for tests only which are silent right now, package
is not presented Guix yet and require a more attention due to complexity.

Build was tested only on x86_64 hardware.

> ./pre-inst-env guix build python-drms python-mpl-animators python-hvpy python-reproject python-sunpy --rounds=2
> /gnu/store/a4afv7qc124szmfn6z08m1c66m3gpv6m-python-sunpy-4.0.6
> /gnu/store/brx97jn7k5iixqpgvkbgl4i3kzyvkm3f-python-reproject-0.9.1
> /gnu/store/f6zbxpvglgq9kj16js2pkw3iy6mmv37m-python-hvpy-1.0.1
> /gnu/store/i143f9pijxs01v280cq6hr1132nafdza-python-mpl-animators-1.1.0
> /gnu/store/f2072k95gjjjfrhjk2rzk158hlp6bdv4-python-drms-0.6.3

Sharlatan Hellseher (5):
  gnu: Add python-drms.
  gnu: Add python-mpl-animators.
  gnu: Add python-hvpy.
  gnu: Add python-reproject.
  gnu: Add python-sunpy.

 gnu/packages/astronomy.scm | 225 +++++++++++++++++++++++++++++++++++++
 1 file changed, 225 insertions(+)


base-commit: 22d44f87763f86a05e9679d9ad2c99e17f4c79be
-- 
2.38.0

[bug#59542] [PATCH 1/5] gnu: Add python-drms.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-drms): New variable.
---
 gnu/packages/astronomy.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d450d1dd94..4ae2e1caa2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1142,6 +1142,43 @@ (define-public python-cdflib
 @end itemize")
     (license license:expat)))
 
+(define-public python-drms
+  (package
+    (name "python-drms")
+    (version "0.6.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "drms" version))
+       (sha256
+        (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key inputs outputs tests?
+                      #:allow-other-keys)
+              (when tests?
+                (add-installed-pythonpath inputs outputs)
+                (setenv "JSOC_EMAIL" "jsoc@sunpy.org")
+                (invoke "python" "-m" "pytest" "-vv")))))))
+    (native-inputs
+     (list python-astropy
+           python-pytest-astropy
+           python-pytest
+           python-setuptools-scm))
+    (propagated-inputs (list python-numpy python-pandas))
+    (home-page "https://sunpy.org")
+    (synopsis "Access astronomical HMI, AIA and MDI data with Python")
+    (description
+     "DRMS module provides an easy-to-use interface for accessing HMI, AIA and MDI
+data with Python.  It uses the publicly accessible
+JSOC (@url{http://jsoc.stanford.edu/}) DRMS server by default, but can also be
+used with local NetDRMS sites.")
+    (license license:bsd-2)))
+
 (define-public python-ephem
   (package
     (name "python-ephem")
-- 
2.38.0

[bug#59542] [PATCH 2/5] gnu: Add python-mpl-animators.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-mpl-animators): New variable.
---
 gnu/packages/astronomy.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4ae2e1caa2..81a051b537 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1202,6 +1202,32 @@ (define-public python-ephem
 of dates.")
     (license license:expat)))
 
+(define-public python-mpl-animators
+  (package
+    (name "python-mpl-animators")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "mpl_animators" version))
+       (sha256
+        (base32 "12kjmj7rn3pk9ly82h5s5hn0kl3kxkr7bgkz9zr9k59pir8z1r8b"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-pytest-mpl
+           python-setuptools-scm))
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy))
+    (home-page "https://sunpy.org")
+    (synopsis "Interactive animations with matplotlib")
+    (description
+     "The @code{mpl_animators} package provides a set of classes which allow the
+easy construction of interactive matplotlib widget based animations.")
+    (license license:bsd-3)))
+
 (define-public python-photutils
   (package
     (name "python-photutils")
-- 
2.38.0

[bug#59542] [PATCH 3/5] gnu: Add python-hvpy.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-hvpy): New variable.
---
 gnu/packages/astronomy.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 81a051b537..eb3b1f01b9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1202,6 +1202,27 @@ (define-public python-ephem
 of dates.")
     (license license:expat)))
 
+(define-public python-hvpy
+  (package
+    (name "python-hvpy")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hvpy" version))
+       (sha256
+        (base32 "0r0asyflz2sw9zn5vgs138nh81m0rbwbakmrncbc1ghdr3g6jahv"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org
+    (propagated-inputs (list python-pydantic python-requests))
+    (native-inputs (list python-pytest python-pytest-astropy))
+    (home-page "https://helioviewer.org/")
+    (synopsis "Helioviewer Python API Wrapper")
+    (description "@code{hvpy} is a Python API wrapper around the formal @url{Helioviewer API,
+https://api.helioviewer.org/docs/v2/}.")
+    (license license:bsd-2)))
+
 (define-public python-mpl-animators
   (package
     (name "python-mpl-animators")
-- 
2.38.0

[bug#59542] [PATCH 4/5] gnu: Add python-reproject.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): New variable.
---
 gnu/packages/astronomy.scm | 56 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index eb3b1f01b9..26d036a0be 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1355,6 +1355,62 @@ (define-public python-regions
     (description "Regions is an Astropy package for region handling.")
     (license license:bsd-3)))
 
+(define-public python-reproject
+  (package
+    (name "python-reproject")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "reproject" version))
+       (sha256
+        (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; FIXME: Failing tests
+      ;;
+      ;; reproject/adaptive/core.py:7: in <module>
+      ;; from .deforest import map_coordinates
+      ;; E   ModuleNotFoundError: No module named 'reproject.adaptive.deforest'
+      ;;
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'writable-compiler
+            (lambda _
+              (make-file-writable "reproject/_compiler.c")))
+          (add-before 'check 'writable-compiler
+            (lambda _
+              (make-file-writable "reproject/_compiler.c")))
+          (add-before 'check 'writable-home
+            (lambda _
+              (setenv "HOME" (getcwd)))))))
+    (propagated-inputs
+     (list python-astropy
+           python-astropy-healpix
+           python-numpy
+           python-pytest
+           python-scipy))
+    (native-inputs
+     (list python-asdf
+           python-cython
+           python-extension-helpers
+           python-gwcs
+           python-pytest-astropy
+           python-pyvo
+           python-semantic-version
+           python-setuptools-scm
+           python-shapely))
+    (home-page "https://reproject.readthedocs.io")
+    (synopsis "Astronomical image reprojection in Python")
+    (description
+     "This package provides a functionality to reproject astronomical images using
+various techniques via a uniform interface, where reprojection is the
+re-gridding of images from one world coordinate system to another e.g.
+changing the pixel resolution, orientation, coordinate system.")
+    (license license:bsd-3)))
+
 (define-public python-astral
   (package
     (name "python-astral")
-- 
2.38.0

[bug#59542] [PATCH 5/5] gnu: Add python-sunpy.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): New variable.
---
 gnu/packages/astronomy.scm | 85 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 26d036a0be..dbe5b4c943 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -36,6 +36,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
@@ -1411,6 +1412,90 @@ (define-public python-reproject
 changing the pixel resolution, orientation, coordinate system.")
     (license license:bsd-3)))
 
+(define-public python-sunpy
+  (package
+    (name "python-sunpy")
+    (version "4.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sunpy" version))
+       (sha256
+        (base32 "0aiirb6l8zshdrpsvh6d5ki759ah9zfm9gbl0in985hprwwxyrq1"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'writable-compiler
+            (lambda _
+              (make-file-writable "sunpy/_compiler.c")))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp")
+              (make-file-writable "sunpy/_compiler.c")
+              ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests
+              (substitute* "sunpy/image/tests/test_transform.py"
+                (("def test_clipping") "def __off_test_clipping")
+                (("def test_nans") "def __off_test_nans")
+                (("def test_endian") "def __off_test_endian"))
+              (substitute* "sunpy/map/tests/test_mapbase.py"
+                (("def test_derotating_nonpurerotation_pcij")
+                 "def __off_test_derotating_nonpurerotation_pcij"))
+              (substitute* "sunpy/map/sources/tests/test_mdi_source.py"
+                (("def test_synoptic_source")
+                 "def __off_test_synoptic_source"))
+              (substitute* "sunpy/tests/tests/test_self_test.py"
+                (("def test_main_nonexisting_module")
+                 "def __off_test_main_nonexisting_module")
+                (("def test_main_stdlib_module")
+                 "def __off_test_main_stdlib_module")))))))
+    (native-inputs
+     (list python-aiohttp
+           python-extension-helpers
+           python-hvpy
+           python-packaging
+           python-pytest
+           python-pytest-astropy
+           python-pytest-doctestplus
+           python-pytest-mock
+           python-pytest-mpl
+           python-pytest-xdist
+           python-setuptools-scm))
+    (propagated-inputs
+     (list parfive
+           python-asdf
+           python-asdf-astropy
+           python-astropy
+           python-beautifulsoup4
+           python-cdflib
+           python-dask
+           python-dateutil
+           python-drms
+           python-glymur
+           python-h5netcdf
+           python-h5py
+           python-hypothesis
+           python-jplephem
+           python-matplotlib
+           python-mpl-animators
+           python-numpy
+           ;; python-opencv-python ; not packed yet
+           python-pandas
+           python-reproject
+           python-scikit-image
+           python-scipy
+           python-semantic-version
+           python-sqlalchemy
+           python-tqdm
+           python-zeep))
+    (home-page "https://sunpy.org")
+    (synopsis "Python library for Solar Physics")
+    (description
+     "SunPy is package for solar physics and is meant to be a free alternative to the
+SolarSoft data analysis environment.")
+    (license license:bsd-2)))
+
 (define-public python-astral
   (package
     (name "python-astral")
-- 
2.38.0

[bug#59542] [PATCH 0/5] gnu: Add python-sunpy.

[Christopher Baines]

[-- Attachment #1: Type: text/plain, Size: 1238 bytes --]


Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> Hi Guix team!
>
> This is the last set of patches which adding with SunPy - solar data analysis
> environment for Python.
>
> python-opencv is required for tests only which are silent right now, package
> is not presented Guix yet and require a more attention due to complexity.
>
> Build was tested only on x86_64 hardware.
>
>> ./pre-inst-env guix build python-drms python-mpl-animators python-hvpy python-reproject python-sunpy --rounds=2
>> /gnu/store/a4afv7qc124szmfn6z08m1c66m3gpv6m-python-sunpy-4.0.6
>> /gnu/store/brx97jn7k5iixqpgvkbgl4i3kzyvkm3f-python-reproject-0.9.1
>> /gnu/store/f6zbxpvglgq9kj16js2pkw3iy6mmv37m-python-hvpy-1.0.1
>> /gnu/store/i143f9pijxs01v280cq6hr1132nafdza-python-mpl-animators-1.1.0
>> /gnu/store/f2072k95gjjjfrhjk2rzk158hlp6bdv4-python-drms-0.6.3
>
> Sharlatan Hellseher (5):
>   gnu: Add python-drms.
>   gnu: Add python-mpl-animators.
>   gnu: Add python-hvpy.
>   gnu: Add python-reproject.
>   gnu: Add python-sunpy.
>
>  gnu/packages/astronomy.scm | 225 +++++++++++++++++++++++++++++++++++++
>  1 file changed, 225 insertions(+)

Thanks! I fixed a couple lint warnings and pushed to master as
78ee6dcfe13c1561ff1d5cdfc2c2d4fa8afe0883.

Chris

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