[bug#53135] [PATCH 0/5] Add some Astropy affiliated packages.

[bug#53135] [PATCH 0/5] Add some Astropy affiliated packages.

[Vinicius Monego]

Vinicius Monego (5):
  gnu: Add python-pyvo.
  gnu: Add python-astroquery.
  gnu: Add python-astropy-healpix.
  gnu: Add python-photutils.
  gnu: Add python-regions.

 gnu/packages/astronomy.scm | 193 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 192 insertions(+), 1 deletion(-)


base-commit: 9d613c36de1ea52e745d30bad841b6cdeaca65f4
-- 
2.30.2

[bug#53135] [PATCH 1/5] gnu: Add python-pyvo.

[Vinicius Monego]

* gnu/packages/astronomy.scm (python-pyvo): New variable.
---
 gnu/packages/astronomy.scm | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a7a07fa3a8..ef85ec79e0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
 ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
-;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
 ;;;
@@ -55,6 +55,7 @@
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-science)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages time)
@@ -705,6 +706,40 @@ much of the core functionality and some common tools needed for performing
 astronomy and astrophysics.")
     (license license:bsd-3)))
 
+(define-public python-pyvo
+  (package
+    (name "python-pyvo")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyvo" version))
+       (sha256
+        (base32 "1lap703wxbyxqlbk85myirp4pkdnc6cg10xhfajfsvz5k0hm5ffw"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "--pyargs" "pyvo" "-k"
+                       (string-append   ; these tests use the network
+                        "not test_access_with_string"
+                        " and not test_access_with_list"
+                        " and not test_access_with_expansion"))))))))
+    (native-inputs
+     (list python-pytest-astropy python-requests-mock))
+    (propagated-inputs
+     (list python-astropy python-mimeparse python-pillow python-requests))
+    (home-page "https://github.com/astropy/pyvo")
+    (synopsis "Access Virtual Observatory data and services")
+    (description
+     "PyVO is a package providing access to remote data and services of the
+Virtual observatory (VO) using Python.")
+    (license license:bsd-3)))
+
 (define-public python-astral
   (package
     (name "python-astral")
-- 
2.30.2

[bug#53135] [PATCH 2/5] gnu: Add python-astroquery.

[Vinicius Monego]

* gnu/packages/astronomy.scm (python-astroquery): New variable.
---
 gnu/packages/astronomy.scm | 44 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ef85ec79e0..ee65fbf2c5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -706,6 +706,50 @@ much of the core functionality and some common tools needed for performing
 astronomy and astrophysics.")
     (license license:bsd-3)))
 
+(define-public python-astroquery
+  (package
+    (name "python-astroquery")
+    (version "0.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astroquery" version))
+       (sha256
+        (base32 "06xy0qzqmps6z5vwfkh5fkhr151p7g94r2j0mvp1rc8zns22y010"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'writable-home
+           (lambda _                    ; some tests need a writable home
+             (setenv "HOME" (getcwd))))
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "--pyargs" "astroquery"
+                       ;; Skip tests that require online data.
+                       "-m" "not remote_data")))))))
+    (propagated-inputs
+     (list python-astropy
+           python-beautifulsoup4
+           python-html5lib
+           python-keyring
+           python-numpy
+           python-pyvo
+           python-requests))
+    (native-inputs
+     (list python-flask
+           python-jinja2
+           python-matplotlib
+           python-pytest-astropy
+           python-pytest-dependency))
+    (home-page "https://www.astropy.org/astroquery/")
+    (synopsis "Access online astronomical data resources")
+    (description "Astroquery is a package that contains a collection of tools
+to access online Astronomical data.  Each web service has its own sub-package.")
+    (license license:bsd-3)))
+
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-- 
2.30.2

[bug#53135] [PATCH 3/5] gnu: Add python-astropy-healpix.

[Vinicius Monego]

* gnu/packages/astronomy.scm (python-astropy-healpix): New variable.
---
 gnu/packages/astronomy.scm | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ee65fbf2c5..1573003c7e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -706,6 +706,45 @@ much of the core functionality and some common tools needed for performing
 astronomy and astrophysics.")
     (license license:bsd-3)))
 
+(define-public python-astropy-healpix
+  (package
+    (name "python-astropy-healpix")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astropy-healpix" version))
+       (sha256
+        (base32 "1436ml03xkmvx4afzbhfj67ab91418sz1w3lq1b18r43qchnd6j0"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This file is opened in both install and check phases.
+         (add-before 'install 'writable-compiler
+           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
+         (add-before 'check 'writable-compiler
+           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               ;; Extensions have to be rebuilt before running the tests.
+               (invoke "python" "setup.py" "build_ext" "--inplace")
+               (invoke "python" "-m" "pytest"
+                       "--pyargs" "astropy_healpix")))))))
+    (native-inputs
+     (list python-extension-helpers
+           python-hypothesis
+           python-pytest-astropy
+           python-setuptools-scm))
+    (propagated-inputs
+     (list python-astropy python-numpy))
+    (home-page "https://github.com/astropy/astropy-healpix")
+    (synopsis "HEALPix for Astropy")
+    (description "This package provides HEALPix to the Astropy project.")
+    (license license:bsd-3)))
+
 (define-public python-astroquery
   (package
     (name "python-astroquery")
-- 
2.30.2

[bug#53135] [PATCH 4/5] gnu: Add python-photutils.

[Vinicius Monego]

* gnu/packages/astronomy.scm (python-photutils): New variable.
---
 gnu/packages/astronomy.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1573003c7e..20961e1436 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -789,6 +789,40 @@ astronomy and astrophysics.")
 to access online Astronomical data.  Each web service has its own sub-package.")
     (license license:bsd-3)))
 
+(define-public python-photutils
+  (package
+    (name "python-photutils")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "photutils" version))
+       (sha256
+        (base32 "1a8djakaya6w5iv9237gkcz39brqzgrfs2wqrl0izi1s85cfdymn"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:test-target "pytest"
+       #:phases
+       (modify-phases %standard-phases
+         ;; This file is opened in both install and check phases.
+         (add-before 'install 'writable-compiler
+           (lambda _ (make-file-writable "photutils/_compiler.c")))
+         (add-before 'check 'writable-compiler
+           (lambda _ (make-file-writable "photutils/_compiler.c"))))))
+    (propagated-inputs
+     (list python-astropy python-numpy))
+    (native-inputs
+     (list python-cython
+           python-extension-helpers
+           python-pytest-astropy
+           python-pytest-runner
+           python-setuptools-scm))
+    (home-page "https://github.com/astropy/photutils")
+    (synopsis "Source detection and photometry")
+    (description "Photutils is an Astropy package for detection and photometry
+of astronomical sources.")
+    (license license:bsd-3)))
+
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-- 
2.30.2

[bug#53135] [PATCH 5/5] gnu: Add python-regions.

[Vinicius Monego]

* gnu/packages/astronomy.scm (python-regions): New variable.
---
 gnu/packages/astronomy.scm | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 20961e1436..e968fd2480 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -857,6 +857,45 @@ of astronomical sources.")
 Virtual observatory (VO) using Python.")
     (license license:bsd-3)))
 
+(define-public python-regions
+  (package
+    (name "python-regions")
+    (version "0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "regions" version))
+       (sha256
+        (base32 "1bjrcjchbw3xw1a26d5g198lh7vxpp9m5sal58r7f8mmr1d8g2dc"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:test-target "pytest"
+       #:phases
+       (modify-phases %standard-phases
+         ;; This doctest requires online data.
+         (add-after 'unpack 'delete-doctest
+           (lambda _ (delete-file "docs/masks.rst")))
+         ;; This file is opened in both install and check phases.
+         (add-before 'install 'writable-compiler
+           (lambda _ (make-file-writable "regions/_compiler.c")))
+         (add-before 'check 'writable-compiler
+           (lambda _ (make-file-writable "regions/_compiler.c")))
+         (add-before 'check 'writable-home
+           (lambda _  (setenv "HOME" (getcwd)))))))
+    (propagated-inputs
+     (list python-astropy python-numpy))
+    (native-inputs
+     (list python-cython
+           python-extension-helpers
+           python-pytest-arraydiff
+           python-pytest-astropy
+           python-pytest-runner
+           python-setuptools-scm))
+    (home-page "https://github.com/astropy/regions")
+    (synopsis "Package for region handling")
+    (description "Regions is an Astropy package for region handling.")
+    (license license:bsd-3)))
+
 (define-public python-astral
   (package
     (name "python-astral")
-- 
2.30.2

bug#53135: [PATCH 0/5] Add some Astropy affiliated packages.

[Ludovic Courtès]

Hi,

Vinicius Monego <monego@posteo.net> skribis:

>   gnu: Add python-pyvo.
>   gnu: Add python-astroquery.
>   gnu: Add python-astropy-healpix.
>   gnu: Add python-photutils.
>   gnu: Add python-regions.

Applied, thanks!

Ludo’.