* [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2.
@ 2023-04-12 20:57 Sharlatan Hellseher
2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher
` (2 more replies)
0 siblings, 3 replies; 16+ messages in thread
From: Sharlatan Hellseher @ 2023-04-12 20:57 UTC (permalink / raw)
To: 62801; +Cc: 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
^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy. 2023-04-12 20:57 [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher @ 2023-04-12 21:05 ` Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher ` (3 more replies) 2023-04-18 20:21 ` [bug#62801] Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2 siblings, 4 replies; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-12 21:05 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler. 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher @ 2023-04-12 21:05 ` Sharlatan Hellseher 2023-04-20 1:52 ` [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Maxim Cournoyer 2023-04-12 21:05 ` [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc Sharlatan Hellseher ` (2 subsequent siblings) 3 siblings, 1 reply; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-12 21:05 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2. 2023-04-12 21:05 ` [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher @ 2023-04-20 1:52 ` Maxim Cournoyer 0 siblings, 0 replies; 16+ messages in thread From: Maxim Cournoyer @ 2023-04-20 1:52 UTC (permalink / raw) To: Sharlatan Hellseher; +Cc: 62801 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 ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc. 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher @ 2023-04-12 21:05 ` Sharlatan Hellseher 2023-04-20 1:55 ` [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Maxim Cournoyer 2023-04-12 21:05 ` [bug#62801] [PATCH 4/4] " Sharlatan Hellseher 2023-04-20 1:48 ` Maxim Cournoyer 3 siblings, 1 reply; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-12 21:05 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2. 2023-04-12 21:05 ` [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc Sharlatan Hellseher @ 2023-04-20 1:55 ` Maxim Cournoyer 0 siblings, 0 replies; 16+ messages in thread From: Maxim Cournoyer @ 2023-04-20 1:55 UTC (permalink / raw) To: Sharlatan Hellseher; +Cc: 62801 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 ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 4/4] gnu: python-astroalign: Update to 2.4.2. 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc Sharlatan Hellseher @ 2023-04-12 21:05 ` Sharlatan Hellseher 2023-04-20 1:58 ` [bug#62801] [PATCH 0/4]: " Maxim Cournoyer 2023-04-20 1:48 ` Maxim Cournoyer 3 siblings, 1 reply; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-12 21:05 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2. 2023-04-12 21:05 ` [bug#62801] [PATCH 4/4] " Sharlatan Hellseher @ 2023-04-20 1:58 ` Maxim Cournoyer 0 siblings, 0 replies; 16+ messages in thread From: Maxim Cournoyer @ 2023-04-20 1:58 UTC (permalink / raw) To: Sharlatan Hellseher; +Cc: 62801 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 ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2. 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher ` (2 preceding siblings ...) 2023-04-12 21:05 ` [bug#62801] [PATCH 4/4] " Sharlatan Hellseher @ 2023-04-20 1:48 ` Maxim Cournoyer 3 siblings, 0 replies; 16+ messages in thread From: Maxim Cournoyer @ 2023-04-20 1:48 UTC (permalink / raw) To: Sharlatan Hellseher; +Cc: 62801 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 ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] 2023-04-12 20:57 [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher @ 2023-04-18 20:21 ` Sharlatan Hellseher 2023-04-24 17:41 ` [bug#62801] Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2 siblings, 1 reply; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-18 20:21 UTC (permalink / raw) To: 62801; +Cc: Maxim Cournoyer 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. ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] 2023-04-18 20:21 ` [bug#62801] Sharlatan Hellseher @ 2023-04-24 17:41 ` Sharlatan Hellseher 2023-05-07 14:40 ` bug#62801: Maxim Cournoyer 0 siblings, 1 reply; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-24 17:41 UTC (permalink / raw) To: 62801; +Cc: Maxim Cournoyer [-- Attachment #1: Type: text/plain, Size: 636 bytes --] 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. > [-- Attachment #2: Type: text/html, Size: 1029 bytes --] ^ permalink raw reply [flat|nested] 16+ messages in thread
* bug#62801: 2023-04-24 17:41 ` [bug#62801] Sharlatan Hellseher @ 2023-05-07 14:40 ` Maxim Cournoyer 0 siblings, 0 replies; 16+ messages in thread From: Maxim Cournoyer @ 2023-05-07 14:40 UTC (permalink / raw) To: Sharlatan Hellseher; +Cc: 62801-done 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 ^ permalink raw reply [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy. 2023-04-12 20:57 [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-18 20:21 ` [bug#62801] Sharlatan Hellseher @ 2023-04-21 20:04 ` Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher ` (2 more replies) 2 siblings, 3 replies; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-21 20:04 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler. 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher @ 2023-04-21 20:04 ` Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 3/4] gnu: Add python-ccdproc Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 4/4] gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher 2 siblings, 0 replies; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-21 20:04 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH v2 3/4] gnu: Add python-ccdproc. 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher @ 2023-04-21 20:04 ` Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 4/4] gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher 2 siblings, 0 replies; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-21 20:04 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
* [bug#62801] [PATCH v2 4/4] gnu: python-astroalign: Update to 2.4.2. 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 3/4] gnu: Add python-ccdproc Sharlatan Hellseher @ 2023-04-21 20:04 ` Sharlatan Hellseher 2 siblings, 0 replies; 16+ messages in thread From: Sharlatan Hellseher @ 2023-04-21 20:04 UTC (permalink / raw) To: 62801; +Cc: 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 ^ permalink raw reply related [flat|nested] 16+ messages in thread
end of thread, other threads:[~2023-05-07 14:41 UTC | newest] Thread overview: 16+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2023-04-12 20:57 [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-12 21:05 ` [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher 2023-04-20 1:52 ` [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Maxim Cournoyer 2023-04-12 21:05 ` [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc Sharlatan Hellseher 2023-04-20 1:55 ` [bug#62801] [PATCH 0/4]: gnu: python-astroalign: Update to 2.4.2 Maxim Cournoyer 2023-04-12 21:05 ` [bug#62801] [PATCH 4/4] " Sharlatan Hellseher 2023-04-20 1:58 ` [bug#62801] [PATCH 0/4]: " Maxim Cournoyer 2023-04-20 1:48 ` Maxim Cournoyer 2023-04-18 20:21 ` [bug#62801] Sharlatan Hellseher 2023-04-24 17:41 ` [bug#62801] Sharlatan Hellseher 2023-05-07 14:40 ` bug#62801: Maxim Cournoyer 2023-04-21 20:04 ` [bug#62801] [PATCH v2 1/4] gnu: Add python-astroscrappy Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 2/4] gnu: Add python-memory-profiler Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 3/4] gnu: Add python-ccdproc Sharlatan Hellseher 2023-04-21 20:04 ` [bug#62801] [PATCH v2 4/4] gnu: python-astroalign: Update to 2.4.2 Sharlatan Hellseher
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