[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[Sharlatan Hellseher]

Hi Guix!

To enable tests I follow the long path to add few more packages. I've noticed
python-memory-profiler is mentioned in this issue
https://issues.guix.gnu.org/60316 which may help to bring homeassistant to
Guix.

> /gnu/store/qnq2rxyaprcd7vy376nh4zcsq7wxv45b-python-astroscrappy-1.1.0
> /gnu/store/w3x2kv12xxzsh6wpd39x05972h3c05md-python-memory-profiler-0.61
> /gnu/store/158nrw23hl78ch7685fs1jvyz7anjbwc-python-ccdproc-2.4.0
> /gnu/store/h9zi371rz32m8bx17fyx465w05yp5fzg-python-astroalign-2.4.2

Sharlatan Hellseher (4):
  gnu: Add python-astroscrappy.
  gnu: Add python-memory-profiler.
  gnu: Add python-ccdproc.
  gnu: python-astroalign: Update to 2.4.2.

 gnu/packages/astronomy.scm    | 111 +++++++++++++++++++++++++++++-----
 gnu/packages/python-check.scm |  49 +++++++++++++++
 2 files changed, 146 insertions(+), 14 deletions(-)


base-commit: 3ab983d630a95a29b9418b1ba8a26e5ca2836ec0
-- 
2.39.2

[bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroscrappy): New variable.
---
 gnu/packages/astronomy.scm | 48 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index db290f5987..f162be6006 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1302,6 +1302,54 @@ (define-public python-astroquery
 to access online Astronomical data.  Each web service has its own sub-package.")
     (license license:bsd-3)))
 
+(define-public python-astroscrappy
+  (package
+    (name "python-astroscrappy")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astroscrappy" version))
+       (sha256
+        (base32 "0shmfilvzpmlwz4fh0bx4kqmzr0y39fgga6vipxb5d1rx1y6q6by"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'preparations
+            (lambda _ (setenv "HOME" "/tmp")))
+          (add-before 'install 'writable-compiler
+            (lambda _ (make-file-writable "astroscrappy/_compiler.c")))
+          (add-before 'check 'writable-compiler
+            (lambda _ (make-file-writable "astroscrappy/_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" "astroscrappy")))))))
+    (native-inputs
+     (list python-cython
+           python-extension-helpers
+           python-h5py
+           python-pandas
+           python-pytest-astropy
+           python-scikit-image
+           python-setuptools-scm
+           python-scipy))
+    (propagated-inputs (list python-astropy python-numpy))
+    (home-page "https://github.com/astropy/astroscrappy")
+    (synopsis "Speedy Cosmic Ray Annihilation Package in Python")
+    (description
+     "Astro-SCRAPPY is designed to detect cosmic rays in images (numpy
+arrays), based on Pieter van Dokkum's L.A.Cosmic algorithm.  Much of this was
+originally adapted from cosmics.py written by Malte Tewes.  This is designed to
+be as fast as possible so some of the readability has been sacrificed,
+specifically in the C code.")
+    (license license:bsd-3)))
+
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-- 
2.39.2

[bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-memory-profiler): New variable.
---
 gnu/packages/python-check.scm | 49 +++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 41a6997190..0affd2896b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1771,6 +1771,55 @@ (define-public python-atpublic
     (license (list license:asl2.0
                    license:lgpl3))))    ; only for setup_helpers.py
 
+(define-public python-memory-profiler
+  (package
+    (name "python-memory-profiler")
+    (version "0.61")
+    (source
+     (origin
+       ;; PyPi tarball lacks tests.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pythonprofilers/memory_profiler")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0n6g47qqmnn7abh3v25535hd8bmfvhf9bnp72m7bkd89f715m7xh"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; XXX: @profile is not loaded in some test files and there are 3 tests
+          ;; which were failed, disable them for now.
+          (add-after 'unpack 'disable-fialing-tests
+            (lambda _
+              (with-directory-excursion "test"
+                (for-each delete-file
+                          '("test_as.py"
+                            "test_func.py"
+                            "test_gen.py"
+                            "test_loop.py"
+                            "test_loop_decorated.py"
+                            "test_mprofile.py"
+                            "test_nested.py"
+                            "test_precision_command_line.py"
+                            "test_unicode.py")))
+              (substitute* "test/test_attributes.py"
+                (("def test_with_profile") "def __off_test_with_profile"))
+              (substitute* "test/test_stream_unicode.py"
+                (("def test_unicode") "def __off_test_unicode"))
+              (substitute* "test/test_tracemalloc.py"
+                (("def test_memory_profiler") "def __off_test_memory_profiler")))))))
+    (native-inputs (list python-pytest-7.1 python-pytest-fixture-config python-safety))
+    (propagated-inputs (list python-psutil))
+    (home-page "https://github.com/pythonprofilers/memory_profiler")
+    (synopsis "Monitor Memory usage of Python code")
+    (description
+     "This package provides a module for monitoring memory usage of a python
+program.")
+    (license license:bsd-3)))
+
 (define-public python-mockito
   (package
     (name "python-mockito")
-- 
2.39.2

[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[Maxim Cournoyer]

Hello,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> * gnu/packages/python-check.scm (python-memory-profiler): New variable.
> ---
>  gnu/packages/python-check.scm | 49 +++++++++++++++++++++++++++++++++++
>  1 file changed, 49 insertions(+)
>
> diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
> index 41a6997190..0affd2896b 100644
> --- a/gnu/packages/python-check.scm
> +++ b/gnu/packages/python-check.scm
> @@ -1771,6 +1771,55 @@ (define-public python-atpublic
>      (license (list license:asl2.0
>                     license:lgpl3))))    ; only for setup_helpers.py
>  
> +(define-public python-memory-profiler
> +  (package
> +    (name "python-memory-profiler")
> +    (version "0.61")
> +    (source
> +     (origin
> +       ;; PyPi tarball lacks tests.
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/pythonprofilers/memory_profiler")
> +             (commit (string-append "v" version))))
> +       (file-name (git-file-name name version))
> +       (sha256
> +        (base32 "0n6g47qqmnn7abh3v25535hd8bmfvhf9bnp72m7bkd89f715m7xh"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          ;; XXX: @profile is not loaded in some test files and there are 3 tests
> +          ;; which were failed, disable them for now.
                      ^fail
                      
> +          (add-after 'unpack 'disable-fialing-tests
                                         ^failing

> +            (lambda _
> +              (with-directory-excursion "test"
> +                (for-each delete-file
> +                          '("test_as.py"
> +                            "test_func.py"
> +                            "test_gen.py"
> +                            "test_loop.py"
> +                            "test_loop_decorated.py"
> +                            "test_mprofile.py"
> +                            "test_nested.py"
> +                            "test_precision_command_line.py"
> +                            "test_unicode.py")))
> +              (substitute* "test/test_attributes.py"
> +                (("def test_with_profile") "def __off_test_with_profile"))
> +              (substitute* "test/test_stream_unicode.py"
> +                (("def test_unicode") "def __off_test_unicode"))
> +              (substitute* "test/test_tracemalloc.py"
> +                (("def test_memory_profiler") "def __off_test_memory_profiler")))))))
> +    (native-inputs (list python-pytest-7.1 python-pytest-fixture-config python-safety))

Please wrap lines to 80 characters.

-- 
Thanks,
Maxim

[bug#62801] [PATCH 3/4] gnu: Add python-ccdproc.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): New variable.
---
 gnu/packages/astronomy.scm | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f162be6006..9961e19695 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
 ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2021, 2022, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -1350,6 +1350,37 @@ (define-public python-astroscrappy
 specifically in the C code.")
     (license license:bsd-3)))
 
+(define-public python-ccdproc
+  (package
+    (name "python-ccdproc")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ccdproc" version))
+       (sha256
+        (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
+     ;; classes are deprecated. Use packaging.version instead.
+     (list #:tests? #f))
+    (native-inputs
+     (list python-memory-profiler python-pytest-astropy))
+    (propagated-inputs
+     (list python-astropy
+           python-astroscrappy
+           python-numpy
+           python-reproject
+           python-scikit-image
+           python-scipy))
+    (home-page "http://ccdproc.readthedocs.io/")
+    (synopsis "Basic data reductions of CCD images")
+    (description "The ccdproc package provides many of the necessary tools for
+processing of CCD images built on a framework to provide error propagation and
+bad pixel tracking throughout the reduction process.")
+    (license license:bsd-3)))
+
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-- 
2.39.2

[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[Maxim Cournoyer]

Hello,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> * gnu/packages/astronomy.scm (python-ccdproc): New variable.
> ---
>  gnu/packages/astronomy.scm | 33 ++++++++++++++++++++++++++++++++-
>  1 file changed, 32 insertions(+), 1 deletion(-)
>
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index f162be6006..9961e19695 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -5,7 +5,7 @@
>  ;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
>  ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
>  ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
> -;;; Copyright © 2021, 2022, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
> +;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
>  ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
>  ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
>  ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
> @@ -1350,6 +1350,37 @@ (define-public python-astroscrappy
>  specifically in the C code.")
>      (license license:bsd-3)))
>  
> +(define-public python-ccdproc
> +  (package
> +    (name "python-ccdproc")
> +    (version "2.4.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (pypi-uri "ccdproc" version))
> +       (sha256
> +        (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
> +     ;; classes are deprecated. Use packaging.version instead.

Please report problem upstream, so that it can be fixed and its
resolution tracked.  If it already is reported, link to it here, with a
"(see: https://...)" trailing bit to the explanatory comment.

> +     (list #:tests? #f))
> +    (native-inputs
> +     (list python-memory-profiler python-pytest-astropy))
> +    (propagated-inputs
> +     (list python-astropy
> +           python-astroscrappy
> +           python-numpy
> +           python-reproject
> +           python-scikit-image
> +           python-scipy))
> +    (home-page "http://ccdproc.readthedocs.io/")
> +    (synopsis "Basic data reductions of CCD images")
> +    (description "The ccdproc package provides many of the necessary tools for
> +processing of CCD images built on a framework to provide error propagation and
> +bad pixel tracking throughout the reduction process.")
> +    (license license:bsd-3)))

Looks fine otherwise!

-- 
Thanks,
Maxim

[bug#62801] [PATCH 4/4] gnu: python-astroalign: Update to 2.4.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroalign): Update to 2.4.2.
  [source]: Use git checkout instead PyPI to enable tests.
  [build-system]: Use pyproject-build-system.
  [propagated-inputs]: Migrate from inputs. Remove labels. Add optional python-bottleneck.
  [native-inputs]: Add python-astropy, python-ccdproc, python-pillow.
---
 gnu/packages/astronomy.scm | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9961e19695..0d7212791a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3070,22 +3070,26 @@ (define-public python-gwcs
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-    (version "2.3.1")
+    (version "2.4.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "astroalign" version))
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/quatrope/astroalign")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "19qzv3552lgrd9qmj0rxs51wmx485hw04cbf76ds5pin85kfaiy1"))))
-    (build-system python-build-system)
-    (arguments
-     ;; TODO: (Sharlatan-20210213T162940+0000): I could not make tests run
-     `(#:tests? #f))
-    (inputs
-     `(("numpy" ,python-numpy)
-       ("scikit-image" ,python-scikit-image)
-       ("scipy" ,python-scipy)
-       ("sep" ,python-sep)))
+        (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-astropy python-ccdproc python-pillow))
+    (propagated-inputs
+     (list python-bottleneck
+           python-numpy
+           python-scikit-image
+           python-scipy
+           python-sep))
     (home-page "https://astroalign.readthedocs.io/")
     (synopsis "Astrometric Alignment of Images")
     (description
-- 
2.39.2

[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[Maxim Cournoyer]

Hello,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> * gnu/packages/astronomy.scm (python-astroalign): Update to 2.4.2.
>   [source]: Use git checkout instead PyPI to enable tests.
>   [build-system]: Use pyproject-build-system.
>   [propagated-inputs]: Migrate from inputs. Remove labels. Add optional python-bottleneck.
>   [native-inputs]: Add python-astropy, python-ccdproc, python-pillow.

There shouldn't be a hanging indent (leading whitespace) in GNU change
logs.  Please wrap lines at 80 chars.

> ---
>  gnu/packages/astronomy.scm | 30 +++++++++++++++++-------------
>  1 file changed, 17 insertions(+), 13 deletions(-)
>
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index 9961e19695..0d7212791a 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -3070,22 +3070,26 @@ (define-public python-gwcs
>  (define-public python-astroalign
>    (package
>      (name "python-astroalign")
> -    (version "2.3.1")
> +    (version "2.4.2")
>      (source
>       (origin
> -       (method url-fetch)
> -       (uri (pypi-uri "astroalign" version))
> +       ;; There are no tests in the PyPI tarball.
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/quatrope/astroalign")
> +             (commit (string-append "v" version))))
> +       (file-name (git-file-name name version))
>         (sha256
> -        (base32 "19qzv3552lgrd9qmj0rxs51wmx485hw04cbf76ds5pin85kfaiy1"))))
> -    (build-system python-build-system)
> -    (arguments
> -     ;; TODO: (Sharlatan-20210213T162940+0000): I could not make tests run
> -     `(#:tests? #f))
> -    (inputs
> -     `(("numpy" ,python-numpy)
> -       ("scikit-image" ,python-scikit-image)
> -       ("scipy" ,python-scipy)
> -       ("sep" ,python-sep)))
> +        (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
> +    (build-system pyproject-build-system)
> +    (native-inputs
> +     (list python-astropy python-ccdproc python-pillow))

This line could fit on one line: (native-inputs (list python-astropy ...))

> +    (propagated-inputs
> +     (list python-bottleneck
> +           python-numpy
> +           python-scikit-image
> +           python-scipy
> +           python-sep))
>      (home-page "https://astroalign.readthedocs.io/")
>      (synopsis "Astrometric Alignment of Images")
>      (description

Well done!  Could you please send a v2 with my smallish comments
addressed? :-)

-- 
Thanks,
Maxim

[bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.

[Maxim Cournoyer]

Hello,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> * gnu/packages/astronomy.scm (python-astroscrappy): New variable.
> ---
>  gnu/packages/astronomy.scm | 48 ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 48 insertions(+)
>
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index db290f5987..f162be6006 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -1302,6 +1302,54 @@ (define-public python-astroquery
>  to access online Astronomical data.  Each web service has its own sub-package.")
>      (license license:bsd-3)))
>  
> +(define-public python-astroscrappy
> +  (package
> +    (name "python-astroscrappy")
> +    (version "1.1.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (pypi-uri "astroscrappy" version))
> +       (sha256
> +        (base32 "0shmfilvzpmlwz4fh0bx4kqmzr0y39fgga6vipxb5d1rx1y6q6by"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'preparations
> +            (lambda _ (setenv "HOME" "/tmp")))
> +          (add-before 'install 'writable-compiler
> +            (lambda _ (make-file-writable "astroscrappy/_compiler.c")))
> +          (add-before 'check 'writable-compiler
> +            (lambda _ (make-file-writable "astroscrappy/_compiler.c")))
> +          (replace 'check
> +            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
> +              (when tests?
> +                (add-installed-pythonpath inputs outputs)

The 'add-install-to-pythonpath' is not needed; this is implicitly
already done before the check phase in the python build systems.

> +                ;; Extensions have to be rebuilt before running the tests.
> +                (invoke "python" "setup.py" "build_ext" "--inplace")

I think it'd be a bit cleaner to move this in a distinct phase named
e.g. 'build-extension.  Then the check phase of pyproject-build-system
could be left alone.  If the '--pyargs' argument is really required, it
can be provided via the #:test-flags #~(list "--pyargs" "astroscrappy")
argument.

> +                (invoke "python" "-m" "pytest" "--pyargs" "astroscrappy")))))))
> +    (native-inputs
> +     (list python-cython
> +           python-extension-helpers
> +           python-h5py
> +           python-pandas
> +           python-pytest-astropy
> +           python-scikit-image
> +           python-setuptools-scm
> +           python-scipy))

The last input should appear earlier (sort).

-- 
Thanks,
Maxim

[bug#62801]

[Sharlatan Hellseher]

Hi,

A gentle ping on this issue, let me know if anything needs to be adjusted.

Regards,
Oleg

-- 
… 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#62801]

[Sharlatan Hellseher]

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Hi Maxim,

I think I've covered all review points.

Thanks,
Oleg

On Tue, 18 Apr 2023, 21:21 Sharlatan Hellseher, <sharlatanus@gmail.com>
wrote:

> Hi,
>
> A gentle ping on this issue, let me know if anything needs to be adjusted.
>
> Regards,
> Oleg
>
> --
> … 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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bug#62801:

[Maxim Cournoyer]

Hi Sharlatan,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> Hi Maxim,
>
> I think I've covered all review points.

Thank you!  I've installed the series, with few minor edits.

-- 
Thanks,
Maxim

[bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroscrappy): 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 97a3255ef9..fb841ed65d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1302,6 +1302,50 @@ (define-public python-astroquery
 to access online Astronomical data.  Each web service has its own sub-package.")
     (license license:bsd-3)))
 
+(define-public python-astroscrappy
+  (package
+    (name "python-astroscrappy")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astroscrappy" version))
+       (sha256
+        (base32 "0shmfilvzpmlwz4fh0bx4kqmzr0y39fgga6vipxb5d1rx1y6q6by"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "--pyargs" "astroscrappy")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'preparations
+            (lambda _ (setenv "HOME" "/tmp")))
+          (add-before 'install 'writable-compiler
+            (lambda _ (make-file-writable "astroscrappy/_compiler.c")))
+          (add-before 'check 'tests-preparation
+            (lambda _
+              (make-file-writable "astroscrappy/_compiler.c")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-cython
+           python-extension-helpers
+           python-h5py
+           python-pandas
+           python-pytest-astropy
+           python-scikit-image
+           python-scipy
+           python-setuptools-scm))
+    (propagated-inputs (list python-astropy python-numpy))
+    (home-page "https://github.com/astropy/astroscrappy")
+    (synopsis "Speedy Cosmic Ray Annihilation Package in Python")
+    (description
+     "Astro-SCRAPPY is designed to detect cosmic rays in images (numpy
+arrays), based on Pieter van Dokkum's L.A.Cosmic algorithm.  Much of this was
+originally adapted from cosmics.py written by Malte Tewes.  This is designed to
+be as fast as possible so some of the readability has been sacrificed,
+specifically in the C code.")
+    (license license:bsd-3)))
+
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-- 
2.39.2

[bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-memory-profiler): New variable.
---
 gnu/packages/python-check.scm | 51 +++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 9ce093697d..f1980a28a9 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1779,6 +1779,57 @@ (define-public python-atpublic
     (license (list license:asl2.0
                    license:lgpl3))))    ; only for setup_helpers.py
 
+(define-public python-memory-profiler
+  (package
+    (name "python-memory-profiler")
+    (version "0.61")
+    (source
+     (origin
+       ;; PyPi tarball lacks tests.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pythonprofilers/memory_profiler")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0n6g47qqmnn7abh3v25535hd8bmfvhf9bnp72m7bkd89f715m7xh"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; XXX: @profile is not loaded in some test files and there are 3
+          ;; tests fail, disable them for now.
+          (add-after 'unpack 'disable-failing-tests
+            (lambda _
+              (with-directory-excursion "test"
+                (for-each delete-file
+                          '("test_as.py"
+                            "test_func.py"
+                            "test_gen.py"
+                            "test_loop.py"
+                            "test_loop_decorated.py"
+                            "test_mprofile.py"
+                            "test_nested.py"
+                            "test_precision_command_line.py"
+                            "test_unicode.py")))
+              (substitute* "test/test_attributes.py"
+                (("def test_with_profile") "def __off_test_with_profile"))
+              (substitute* "test/test_stream_unicode.py"
+                (("def test_unicode") "def __off_test_unicode"))
+              (substitute* "test/test_tracemalloc.py"
+                (("def test_memory_profiler")
+                 "def __off_test_memory_profiler")))))))
+    (native-inputs
+     (list python-pytest-7.1 python-pytest-fixture-config python-safety))
+    (propagated-inputs (list python-psutil))
+    (home-page "https://github.com/pythonprofilers/memory_profiler")
+    (synopsis "Monitor Memory usage of Python code")
+    (description
+     "This package provides a module for monitoring memory usage of a python
+program.")
+    (license license:bsd-3)))
+
 (define-public python-mockito
   (package
     (name "python-mockito")
-- 
2.39.2

[bug#62801] [PATCH v2 3/4] gnu: Add python-ccdproc.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): New variable.
---
 gnu/packages/astronomy.scm | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fb841ed65d..086bf8d69f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
 ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2021, 2022, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -1346,6 +1346,38 @@ (define-public python-astroscrappy
 specifically in the C code.")
     (license license:bsd-3)))
 
+(define-public python-ccdproc
+  (package
+    (name "python-ccdproc")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ccdproc" version))
+       (sha256
+        (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
+     ;; classes are deprecated. Use packaging.version instead.
+     ;; (see https://github.com/astropy/ccdproc/issues/805)
+     (list #:tests? #f))
+    (native-inputs
+     (list python-memory-profiler python-pytest-astropy))
+    (propagated-inputs
+     (list python-astropy
+           python-astroscrappy
+           python-numpy
+           python-reproject
+           python-scikit-image
+           python-scipy))
+    (home-page "http://ccdproc.readthedocs.io/")
+    (synopsis "Basic data reductions of CCD images")
+    (description "The ccdproc package provides many of the necessary tools for
+processing of CCD images built on a framework to provide error propagation and
+bad pixel tracking throughout the reduction process.")
+    (license license:bsd-3)))
+
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-- 
2.39.2

[bug#62801] [PATCH v2 4/4] gnu: python-astroalign: Update to 2.4.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroalign): Update to 2.4.2.
[source]: Use git checkout instead PyPI to enable tests.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Migrate from inputs. Remove labels. Add optional
python-bottleneck.
[native-inputs]: Add python-astropy, python-ccdproc, python-pillow.
---
 gnu/packages/astronomy.scm | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 086bf8d69f..d02f74b196 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3067,22 +3067,25 @@ (define-public python-gwcs
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-    (version "2.3.1")
+    (version "2.4.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "astroalign" version))
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/quatrope/astroalign")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "19qzv3552lgrd9qmj0rxs51wmx485hw04cbf76ds5pin85kfaiy1"))))
-    (build-system python-build-system)
-    (arguments
-     ;; TODO: (Sharlatan-20210213T162940+0000): I could not make tests run
-     `(#:tests? #f))
-    (inputs
-     `(("numpy" ,python-numpy)
-       ("scikit-image" ,python-scikit-image)
-       ("scipy" ,python-scipy)
-       ("sep" ,python-sep)))
+        (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-astropy python-ccdproc python-pillow))
+    (propagated-inputs
+     (list python-bottleneck
+           python-numpy
+           python-scikit-image
+           python-scipy
+           python-sep))
     (home-page "https://astroalign.readthedocs.io/")
     (synopsis "Astrometric Alignment of Images")
     (description
-- 
2.39.2