GNU bug report logs - #63806
[PATCH 00/18]: gnu: Add JWST (James Webb Space Telescope)

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 00/18]: gnu: Add JWST (James Webb Space Telescope)
Date: Tue, 30 May 2023 20:39:37 +0100

Hi Guix!

Finally!

It's packed, linted, styled, build adjusted and ready for review.

This patch set provides rest of the missing inputs for python-jwst. Some of
the test suites are silent due to requirements of Internet access to remote
data servers, some needs more love to figure out the reason.

Regards,
Oleg

Sharlatan Hellseher (18):
  gnu: Add python-pysynshot.
  gnu: Add python-rad.
  gnu: Add python-roman-datamodels.
  gnu: Add python-stsci-image.
  gnu: Add python-stsci-imagestats.
  gnu: Add python-stsci-stimage.
  gnu: Add python-tweakwcs.
  gnu: Add python-synphot.
  gnu: Add python-stsynphot.
  gnu: Add python-parsley.
  gnu: Add python-crds.
  gnu: Add python-stdatamodels.
  gnu: Add python-stpipe.
  gnu: Add python-bayesicfitting.
  gnu: Add python-wiimatch.
  gnu: Add python-drizzle.
  gnu: Add python-stcal.
  gnu: Add python-jwst.

 gnu/packages/astronomy.scm  | 590 ++++++++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm |  30 ++
 2 files changed, 620 insertions(+)


base-commit: 7b400e7f8751e6b0cc6e66d3f7ecfb7f5bd51309
-- 
2.40.1

Message #8 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 02/18] gnu: Add python-rad.
Date: Tue, 30 May 2023 20:58:32 +0100

* gnu/packages/astronomy.scm (python-rad): New variable.
---
 gnu/packages/astronomy.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5429cceeae..359704f8dd 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3082,6 +3082,36 @@ (define-public python-gwcs
 default) to world coordinates.")
     (license license:bsd-3)))
 
+(define-public python-rad
+  (package
+    (name "python-rad")
+    (version "0.15.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "rad" version))
+              (sha256
+               (base32
+                "0j51pkywxdaqrfz162rdsywlvx1mbb2h0gi5framvhf25i1im7mb"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags #~(list "-k" "not remote_data")))
+    (native-inputs (list python-astropy
+                         python-pytest
+                         python-pytest-doctestplus
+                         python-pytest-openfiles
+                         python-semantic-version
+                         python-setuptools-scm))
+    (propagated-inputs (list python-asdf python-asdf-astropy))
+    (home-page "https://github.com/spacetelescope/rad")
+    (synopsis "Roman Attribute Dictionary")
+    (description
+     "@acronym{RAD, The Roman Attribute Dictionary} is package which defines schemas
+for the Nancy Grace Roman Space Telescope shared attributes for processing and
+archive.  These schemas are schemas for the ASDF file file format, which are used
+by ASDF to serialize and deserialize data for the Nancy Grace Roman Space
+Telescope.")
+    (license license:bsd-3)))
+
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-- 
2.40.1

Message #11 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 01/18] gnu: Add python-pysynshot.
Date: Tue, 30 May 2023 20:58:31 +0100

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

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 964e72642c..5429cceeae 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2687,6 +2687,38 @@ (define-public python-pynbody
 N-Chilada and RAMSES AMR outputs.")
     (license license:gpl3+)))
 
+(define-public python-pysynphot
+  (package
+    (name "python-pysynphot")
+    (version "2.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pysynphot" version))
+              (sha256
+               (base32
+                "1rr29m63bnj47f6gvbvg3pm1296x14ad29c6qd0sdj4f4ilrzhj5"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-before 'check 'set-env-data-path
+                          (lambda _
+                            (setenv "PYSYN_CDBS"
+                                    (string-append #$output "/crds")))))))
+    (native-inputs (list python-pytest python-pytest-remotedata
+                         python-setuptools-scm))
+    (propagated-inputs (list python-astropy python-beautifulsoup4 python-numpy
+                             python-pytest-astropy-header python-six))
+    (home-page "https://github.com/spacetelescope/pysynphot")
+    (synopsis "Python Synthetic Photometry Utilities")
+    (description
+     "Astrolib PySynphot (hereafter referred to only as pysynphot) is an
+object-oriented replacement for STSDAS SYNPHOT synthetic photometry package in
+IRAF.  @code{pysynphot} simulates photometric data and spectra as they are observed
+with the Hubble Space Telescope (HST). Passbands for standard photometric
+systems are available, and users can incorporate their own filters, spectra, and
+data.")
+    (license license:bsd-3)))
+
 (define-public python-sep
   (package
     (inherit libsep)
-- 
2.40.1

Message #14 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 03/18] gnu: Add python-roman-datamodels.
Date: Tue, 30 May 2023 20:58:33 +0100

* gnu/packages/astronomy.scm (python-roman-datamodels): New variable.
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 359704f8dd..231a4cf58b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3112,6 +3112,48 @@ (define-public python-rad
 Telescope.")
     (license license:bsd-3)))
 
+(define-public python-roman-datamodels
+  (package
+    (name "python-roman-datamodels")
+    (version "0.15.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "roman_datamodels" version))
+              (sha256
+               (base32
+                "0frhm1cqqd8934yizhm4fy78y38q2w9ncm4rv1n74hfypkyis4ap"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; XXX: Check how to make all tests enabled, probably some more inner
+     ;; input chain needs to be upgraded, keep them disabled to make the build
+     ;; green.
+     (list #:test-flags #~(list "-k"
+                                (string-append "not test_will_validate"
+                                 " and not test_will_strict_validate"
+                                 " and not test_nuke_validation"))))
+    (propagated-inputs (list python-asdf
+                             python-asdf-astropy
+                             python-asdf-standard
+                             python-astropy
+                             python-gwcs
+                             python-numpy
+                             python-psutil
+                             python-rad))
+    (native-inputs (list python-pytest python-pytest-doctestplus
+                         python-pytest-openfiles python-semantic-version
+                         python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/roman_datamodels")
+    (synopsis "Roman Datamodels Support")
+    (description
+     "This package provides a Python pacakge of Roman Datamodels for the
+calibration pipelines started with the JWST calibration pipelines.  The goal
+for the JWST pipelines was motivated primarily by the need to support FITS
+data files, specifically with isolating the details of where metadata and data
+were located in the FITS file from the representation of the same items within
+the Python code.  That is not a concern for Roman since FITS format data files
+will not be used by the Roman calibration pipelines.")
+    (license license:bsd-3)))
+
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-- 
2.40.1

Message #17 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 04/18] gnu: Add python-stsci-image.
Date: Tue, 30 May 2023 20:58:34 +0100

* gnu/packages/astronomy.scm (python-stsci-image): New variable.
---
 gnu/packages/astronomy.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 231a4cf58b..e2a8796149 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2045,6 +2045,34 @@ (define-public python-spherical-geometry
     ;; QD_LIBRARY_LICENSE.rst for bandeled QD source
     (license license:bsd-3)))
 
+(define-public python-stsci-image
+  (package
+    (name "python-stsci-image")
+    (version "2.3.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stsci.image" version))
+              (sha256
+               (base32
+                "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-before 'check 'build-extensions
+                          (lambda _
+                            ;; Cython extensions have to be built before running
+                            ;; the tests.
+                            (invoke "python" "setup.py" "build_ext"
+                                    "--inplace"))))))
+    (propagated-inputs (list python-numpy python-scipy))
+    (native-inputs (list python-pytest python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stsci.image")
+    (synopsis "Image array manipulation functions")
+    (description
+     "This package provides Python modules of @acronym{STScI, Space Telescope Science
+Institute} image array manipulation functions")
+    (license license:bsd-3)))
+
 (define-public libnova
   (package
     (name "libnova")
-- 
2.40.1

Message #20 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 05/18] gnu: Add python-stsci-imagestats.
Date: Tue, 30 May 2023 20:58:35 +0100

* gnu/packages/astronomy.scm (python-stsci-imagestats): New variable.
---
 gnu/packages/astronomy.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e2a8796149..41e79205ba 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2073,6 +2073,29 @@ (define-public python-stsci-image
 Institute} image array manipulation functions")
     (license license:bsd-3)))
 
+(define-public python-stsci-imagestats
+  (package
+    (name "python-stsci-imagestats")
+    (version "1.6.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stsci.imagestats" version))
+              (sha256
+               (base32
+                "14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:tests? #f)) ;No teests
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stsci.imagestats")
+    (synopsis "Compute sigma-clipped statistics on data arrays")
+    (description
+     "@code{stsci.imagestats} is a package designed to compute various statistics on
+image data using sigma-clipping iterations.  It is designed to replicate core
+behaviour of the IRAF's")
+    (license license:bsd-3)))
+
 (define-public libnova
   (package
     (name "libnova")
-- 
2.40.1

Message #23 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 06/18] gnu: Add python-stsci-stimage.
Date: Tue, 30 May 2023 20:58:36 +0100

* gnu/packages/astronomy.scm (python-stsci-stimage): New variable.
---
 gnu/packages/astronomy.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 41e79205ba..2b0cd113e5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2096,6 +2096,30 @@ (define-public python-stsci-imagestats
 behaviour of the IRAF's")
     (license license:bsd-3)))
 
+(define-public python-stsci-stimage
+  (package
+    (name "python-stsci-stimage")
+    (version "0.2.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stsci.stimage" version))
+              (sha256
+               (base32
+                "0i7xby1gaiplvbqqv8a4f4cw1is8fwj89mix1z3bqrykqi3n24g0"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Fix failing tests. There are errors to load test files.
+      #:tests? #f))
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-codecov python-pytest python-pytest-cov
+                         python-setuptools-scm))
+    (home-page "https://stscistimage.readthedocs.io/en/latest/")
+    (synopsis "STScI image processing")
+    (description "This package provides an astronomical Python package with
+image processing functions: @code{xyxymatch}, @code{geomap}.")
+    (license license:bsd-3)))
+
 (define-public libnova
   (package
     (name "libnova")
-- 
2.40.1

Message #26 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 07/18] gnu: Add python-tweakwcs.
Date: Tue, 30 May 2023 20:58:37 +0100

* gnu/packages/astronomy.scm (python-tweakwcs): 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 2b0cd113e5..c2df8eae69 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2830,6 +2830,40 @@ (define-public python-suntime
 datetime object.")
     (license license:lgpl3+)))
 
+(define-public python-tweakwcs
+  (package
+    (name "python-tweakwcs")
+    (version "0.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "tweakwcs" version))
+              (sha256
+               (base32
+                "1500w737n9vf5hv16xkybk4shl7g4wfzb2ji9mc4vgzj41gkrwl4"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-astropy
+                             python-gwcs
+                             python-numpy
+                             python-packaging
+                             python-spherical-geometry
+                             python-stsci-imagestats
+                             python-stsci-stimage))
+    (native-inputs (list python-codecov
+                         python-pytest
+                         python-pytest-cov
+                         python-scipy
+                         python-semantic-version
+                         python-setuptools-scm))
+    (home-page "https://tweakwcs.readthedocs.io/en/latest/")
+    (synopsis
+     "Algorithms for matching and aligning catalogs and for tweaking the WCS")
+    (description
+     "@code{tweakwcs} is a package that provides core algorithms for computing and
+applying corrections to @code{WCS} objects such as to minimize mismatch between
+image and reference catalogs. Currently only aligning images with @code{FITS
+WCS} and @code{JWST gWCS} are supported.")
+    (license license:bsd-3)))
+
 (define-public python-asdf
   (package
     (name "python-asdf")
-- 
2.40.1

Message #29 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 09/18] gnu: Add python-stsynphot.
Date: Tue, 30 May 2023 20:58:39 +0100

* gnu/packages/astronomy.scm (python-stsynphot): 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 9373eaed40..5b673350ba 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2120,6 +2120,40 @@ (define-public python-stsci-stimage
 image processing functions: @code{xyxymatch}, @code{geomap}.")
     (license license:bsd-3)))
 
+(define-public python-stsynphot
+  (package
+    (name "python-stsynphot")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stsynphot" version))
+              (sha256
+               (base32
+                "0qkdh47j84v7fzri7bmi1jcmggdqq0a8byamfm73d8mbz86v8sn4"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests fails on missing file, it might need to be downloaded,
+      ;; disable them for now.  astropy.utils.exceptions.AstropyUserWarning:
+      ;; Failed to load Vega spectrum from
+      ;; /grp/redcat/trds/calspec/alpha_lyr_stis_010.fits;
+      #:tests? #f))
+    (propagated-inputs (list python-astropy
+                             python-beautifulsoup4
+                             python-matplotlib
+                             python-numpy
+                             python-scipy
+                             python-synphot))
+    (native-inputs (list python-pytest python-pytest-astropy
+                         python-pytest-astropy-header python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stsynphot_refactor")
+    (synopsis "Synthetic photometry using Astropy for HST and JWST")
+    (description
+     "This package provides a replacement for IRAF STSDAS SYNPHOT
+and ASTROLIB PYSYNPHOT, utilizing Astropy covering instrument specific portions
+of the old packages for HST.")
+    (license license:bsd-3)))
+
 (define-public libnova
   (package
     (name "libnova")
-- 
2.40.1

Message #32 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 08/18] gnu: Add python-synphot.
Date: Tue, 30 May 2023 20:58:38 +0100

* gnu/packages/astronomy.scm (python-synphot): New variable.
---
 gnu/packages/astronomy.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c2df8eae69..9373eaed40 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2830,6 +2830,35 @@ (define-public python-suntime
 datetime object.")
     (license license:lgpl3+)))
 
+(define-public python-synphot
+  (package
+    (name "python-synphot")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "synphot" version))
+              (sha256
+               (base32
+                "02pjp1bnbyq7zi1bxqv56nif4ijd8fscmnn9ldrs8yvgsbmgdvlc"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Test needs more love to pass.
+      ;;
+      ;; ERROR collecting synphot/tests/test_utils.py
+      ;;
+      #:tests? #f))
+    (propagated-inputs (list python-astropy python-numpy python-scipy))
+    (native-inputs (list python-pytest python-pytest-astropy
+                         python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/synphot_refactor")
+    (synopsis "Synthetic photometry using Astropy")
+    (description
+     "This package provides a replacement for IRAF STSDAS SYNPHOT and ASTROLIB
+PYSYNPHOT, utilizing Astropy and covering the non-instrument specific portions
+of the old packages.")
+    (license license:bsd-3)))
+
 (define-public python-tweakwcs
   (package
     (name "python-tweakwcs")
-- 
2.40.1

Message #35 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 11/18] gnu: Add python-crds.
Date: Tue, 30 May 2023 20:58:41 +0100

* gnu/packages/astronomy.scm (python-crds): New variable.
---
 gnu/packages/astronomy.scm | 52 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5b673350ba..d5fb41f7c4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1425,6 +1425,58 @@ (define-public python-cdflib
 @end itemize")
     (license license:expat)))
 
+(define-public python-crds
+  (package
+    (name "python-crds")
+    (version "11.17.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "crds" version))
+              (sha256
+               (base32
+                "0sdz1k4hrgrc2jwihp9ns7lx23kcz7f90c222q7aaqf9g3vvpqlr"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests require Internet access to https://hst-crds.stsci.edu and
+      ;; additional test data. See:
+      ;; https://github.com/spacetelescope/crds/blob/master/setup_test_cache
+      #:tests? #f))
+    (propagated-inputs (list python-asdf
+                             python-astropy
+                             python-boto3
+                             python-filelock
+                             python-lxml
+                             python-numpy
+                             python-parsley
+                             python-pysynphot
+                             python-roman-datamodels
+                             python-stsynphot
+                             python-requests))
+    (native-inputs (list python-flake8
+                         python-ipython
+                         python-lockfile
+                         python-mock
+                         python-nose
+                         python-pylint
+                         python-pytest
+                         python-semantic-version
+                         python-setuptools-scm))
+    (home-page "https://hst-crds.stsci.edu")
+    (synopsis "Calibration Reference Data System for HST and JWST")
+    (description
+     "CRDS is a package used for working with astronomical reference files for
+the HST and JWST telescopes.  CRDS is useful for performing various operations on
+reference files or reference file assignment rules.  CRDS is used to assign,
+check, and compare reference files and rules, and also to predict those datasets
+which should potentially be reprocessed due to changes in reference files or
+assignment rules.  CRDS has versioned rules which define the assignment of
+references for each type and instrument configuration.  CRDS has web sites
+corresponding to each project (http://hst-crds.stsci.edu or
+https://jwst-crds.stsci.edu/) which record information about reference files and
+provide related services.")
+    (license license:bsd-3)))
+
 (define-public python-czml3
   (package
     (name "python-czml3")
-- 
2.40.1

Message #38 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 10/18] gnu: Add python-parsley.
Date: Tue, 30 May 2023 20:58:40 +0100

* gnu/packages/python-xyz.scm (python-parsley): New variable.
---
 gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f7e3f6f538..b8ee05df05 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3811,6 +3811,36 @@ (define-public python-parse
 syntax.")
     (license license:x11)))
 
+(define-public python-parsley
+  (package
+    (name "python-parsley")
+    (version "1.3")
+    (source (origin
+              ;; The source distributed on PyPI is outdated.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pyga/parsley")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0550rw65ygqzbjc8a66hs355pzbx727kbn20dssdb6ls846gw2qs"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Check why these 3 tests fail.
+      #:test-flags #~(list "-k"
+                           (string-append "not test_sending_empty_netstring"
+                            " and not test_sending_one_netstring"
+                            " and not test_sending_two_netstrings"))))
+    (native-inputs (list python-pytest python-twisted))
+    (home-page "https://launchpad.net/parsley")
+    (synopsis "Parsing and pattern matching Python library")
+    (description
+     "Parsley is an implementation of OMeta, an object-oriented pattern-matching
+language developed by Alessandro Warth at http://tinlizzie.org/ometa/")
+    (license license:expat)))
+
 (define-public python-polib
   (package
     (name "python-polib")
-- 
2.40.1

Message #41 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 12/18] gnu: Add python-stdatamodels.
Date: Tue, 30 May 2023 20:58:42 +0100

* gnu/packages/astronomy.scm (python-stdatamodels): New variable.
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d5fb41f7c4..6f5d06f634 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2172,6 +2172,48 @@ (define-public python-stsci-stimage
 image processing functions: @code{xyxymatch}, @code{geomap}.")
     (license license:bsd-3)))
 
+(define-public python-stdatamodels
+  (package
+    (name "python-stdatamodels")
+    (version "1.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stdatamodels" version))
+              (sha256
+               (base32
+                "1lssz5mnkzgraqa9mdg1w39scsikymcp3zpmsjb146r0pqnwnpzw"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Disable tests requiring access to CRDS servers to download ~500MiB
+      ;; of data.
+      #:test-flags #~(list "-k" "not test_crds_selectors_vs_datamodel")
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'check 'set-home
+                     (lambda _
+                       (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list python-asdf
+                             python-asdf-astropy
+                             python-astropy
+                             python-jsonschema
+                             python-numpy
+                             python-psutil))
+    (native-inputs (list python-crds
+                         python-pytest
+                         python-pytest-doctestplus
+                         python-pytest-openfiles
+                         python-scipy
+                         python-semantic-version
+                         python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stdatamodels")
+    (synopsis
+     "Core support for DataModel classes used in calibration pipelines")
+    (description
+     "Provides DataModel, which is the base class for data models implemented in the
+@acronym{JWST, James Webb Space Telescope} and @acronym{Roman, Nancy Grace Roman
+Space Telescope} calibration software.")
+    (license license:bsd-3)))
+
 (define-public python-stsynphot
   (package
     (name "python-stsynphot")
-- 
2.40.1

Message #44 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 13/18] gnu: Add python-stpipe.
Date: Tue, 30 May 2023 20:58:43 +0100

* gnu/packages/astronomy.scm (python-stpipe): New variable.
---
 gnu/packages/astronomy.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6f5d06f634..cb6018c588 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2214,6 +2214,29 @@ (define-public python-stdatamodels
 Space Telescope} calibration software.")
     (license license:bsd-3)))
 
+(define-public python-stpipe
+  (package
+    (name "python-stpipe")
+    (version "0.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stpipe" version))
+              (sha256
+               (base32
+                "17gnwzhl10vbg059lfprdyci19dlh3whkmb9rl7z25wr593rnvcp"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-asdf python-astropy python-crds
+                             python-semantic-version python-stdatamodels))
+    (native-inputs (list python-pytest python-pytest-doctestplus
+                         python-pytest-openfiles python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stpipe")
+    (synopsis "Framework for calibration pipeline software")
+    (description
+     "This package provides base classes and command-line tools for
+implementing calibration pipeline software.")
+    ;; LICENSE Association of Universities for Research in Astronomy (AURA)
+    (license license:bsd-3)))
+
 (define-public python-stsynphot
   (package
     (name "python-stsynphot")
-- 
2.40.1

Message #47 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 14/18] gnu: Add python-bayesicfitting.
Date: Tue, 30 May 2023 20:58:44 +0100

* gnu/packages/astronomy.scm (python-bayesicfitting): New variable.
---
 gnu/packages/astronomy.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cb6018c588..bb90801408 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1355,6 +1355,37 @@ (define-public python-astroscrappy
 specifically in the C code.")
     (license license:bsd-3)))
 
+(define-public python-bayesicfitting
+  (package
+    (name "python-bayesicfitting")
+    (version "3.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dokester/BayesicFitting")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "07y9dr9wxhxrvhk0jjakhbyrgal60i92m7z7q14fp12k8x0gl69l"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (replace 'check
+                          (lambda* (#:key tests? #:allow-other-keys)
+                            (when tests?
+                              (invoke "python" "-m" "unittest" "discover"
+                                      "test")))))))
+    (propagated-inputs (list python-astropy python-future python-matplotlib
+                             python-numpy python-scipy))
+    (home-page "https://www.bayesicfitting.nl")
+    (synopsis "Python Toolbox for Astronimical Bayesian fitting")
+    (description
+     "The BayesicFitting package is a python version of the the fitter classes
+in Herschel Common Science System (HCSS).  HCSS was the all encompassing software
+system for the operations and analysis of the ESA satelite Herschel.")
+    (license license:gpl3+)))
+
 (define-public python-ccdproc
   (package
     (name "python-ccdproc")
-- 
2.40.1

Message #50 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 15/18] gnu: Add python-wiimatch.
Date: Tue, 30 May 2023 20:58:45 +0100

* gnu/packages/astronomy.scm (python-wiimatch): New variable.
---
 gnu/packages/astronomy.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bb90801408..4f94722ce6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3526,3 +3526,26 @@ (define-public python-skyfield
      "Skyfield computes positions for the stars, planets, and satellites in
 orbit around the Earth.")
     (license license:expat)))
+
+(define-public python-wiimatch
+  (package
+    (name "python-wiimatch")
+    (version "0.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "wiimatch" version))
+              (sha256
+               (base32
+                "0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy python-scipy))
+    (native-inputs (list python-codecov python-pytest python-pytest-cov
+                         python-pytest-doctestplus python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/wiimatch")
+    (synopsis
+     "Optimal matching of weighted N-dimensional image intensity data")
+    (description
+     "@code{wiimatch} is a package that provides core computational algorithms for
+optimal @code{matching} of weighted N-dimensional image intensity data
+using (multivariate) polynomials.")
+    (license license:bsd-3)))
-- 
2.40.1

Message #53 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 16/18] gnu: Add python-drizzle.
Date: Tue, 30 May 2023 20:58:46 +0100

* gnu/packages/astronomy.scm (python-drizzle): New variable.
---
 gnu/packages/astronomy.scm | 47 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4f94722ce6..26a67670b4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1576,6 +1576,53 @@ (define-public python-drms
 used with local NetDRMS sites.")
     (license license:bsd-2)))
 
+(define-public python-drizzle
+  (package
+    (name "python-drizzle")
+    (version "1.13.7")
+    (source (origin
+              (method git-fetch) ;PyPi has not test data sets
+              (uri (git-reference
+                    (url "https://github.com/spacetelescope/drizzle")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0x591d9gjasds91fvwcf37bhxp5nra28g0vq5zkykczpc70ywiy8"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: 2 of 26 tests failed with AssertionError, disable them for now.
+      ;; Consider mention it in upstream.
+      #:test-flags #~(list "-k"
+                           (string-append "not test_square_with_point"
+                                          " and not test_square_with_grid"))
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'build 'set-env-version
+                     (lambda _
+                       (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                               #$version)))
+                   (add-before 'check 'build-extensions
+                     (lambda _
+                       ;; Cython extensions have to be built before running
+                       ;; the tests.
+                       (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs (list python-astropy python-numpy))
+    (native-inputs (list python-coverage python-flake8 python-pytest
+                         python-pytest-cov python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/drizzle")
+    (synopsis
+     "Astronomical tool for combining dithered images into a single image")
+    (description
+     "The drizzle library is a Python package for combining dithered images into
+a single image.  This library is derived from code used in DrizzlePac.  Like
+DrizzlePac, most of the code is implemented in the C language.  The biggest
+change from DrizzlePac is that this code passes an array that maps the input to
+output image into the C code, while the DrizzlePac code computes the mapping by
+using a Python callback.  Switching to using an array allowed the code to be
+greatly simplified.")
+    (license license:bsd-3)))
+
 (define-public python-ephem
   (package
     (name "python-ephem")
-- 
2.40.1

Message #56 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 17/18] gnu: Add python-stcal.
Date: Tue, 30 May 2023 20:58:47 +0100

* gnu/packages/astronomy.scm (python-stcal): New variable.
---
 gnu/packages/astronomy.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 26a67670b4..475362c8bb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2250,6 +2250,35 @@ (define-public python-stsci-stimage
 image processing functions: @code{xyxymatch}, @code{geomap}.")
     (license license:bsd-3)))
 
+(define-public python-stcal
+  (package
+    (name "python-stcal")
+    (version "1.3.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stcal" version))
+              (sha256
+               (base32
+                "0yy0pwi3krvhxfby6nzgpgyz5il3sl1j29ihbk81dh9fdh3ys2n9"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        ;; XXX: Can't detect opencv-python version. The input
+                        ;; opencv might not set the version correctly.
+                        (delete 'sanity-check))))
+    (propagated-inputs (list opencv ;Provides OpenCV-Python
+                             python-astropy python-numpy python-scipy))
+    (native-inputs (list python-psutil
+                         python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-pytest-openfiles
+                         python-setuptools-scm))
+    (home-page "https://github.com/spacetelescope/stcal")
+    (synopsis "STScI tools and algorithms used in calibration pipelines")
+    (description "STScI tools and algorithms used in calibration pipelines")
+    (license license:bsd-3)))
+
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-- 
2.40.1

Message #59 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 18/18] gnu: Add python-jwst.
Date: Tue, 30 May 2023 20:58:48 +0100

* gnu/packages/astronomy.scm (python-jwst): New variable.
---
 gnu/packages/astronomy.scm | 67 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 475362c8bb..2772e58141 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2923,6 +2923,73 @@ (define-public python-jplephem
 JPL ephemerides use to predict raw (x,y,z) planetary positions.")
     (license license:expat)))
 
+(define-public python-jwst
+  (package
+    (name "python-jwst")
+    (version "1.10.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "jwst" version))
+              (sha256
+               (base32
+                "1lmfyw2y7c84rs9xqavah9aidj478ijiiijlz6fag11xqn1vs98y"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests require access to https://jwst-crds-pub.stsci.edu server for
+      ;; getting data sets.
+      #:tests? #f
+      #:phases #~(modify-phases %standard-phases
+                   ;; NOTE: (Sharlatan-20230529T113448+0100): opencv-python's
+                   ;; version can't be detected, it could the way it's packed in
+                   ;; Guix. Review failing sanity check with more efforts,
+                   ;; disable for now to make package buildable.
+                   (delete 'sanity-check))))
+    ;; opencv provides OpenCV-Python which is Listed as install requirement.
+    (propagated-inputs (list opencv
+                             python-asdf
+                             python-asdf-astropy
+                             python-astropy
+                             python-bayesicfitting
+                             python-crds
+                             python-drizzle
+                             python-gwcs
+                             python-jsonschema
+                             python-numpy
+                             python-photutils
+                             python-poppy
+                             python-psutil
+                             python-pyparsing
+                             python-requests
+                             python-scikit-image
+                             python-scipy
+                             python-spherical-geometry
+                             python-stcal
+                             python-stdatamodels
+                             python-stpipe
+                             python-stsci-image
+                             python-stsci-imagestats
+                             python-tweakwcs
+                             python-wiimatch))
+    (native-inputs (list python-codecov
+                         python-colorama
+                         python-flake8
+                         python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-pytest-openfiles
+                         python-requests-mock
+                         python-setuptools-scm))
+    (home-page "https://jwst-pipeline.readthedocs.io/en/latest/")
+    (synopsis
+     "Python library for science observations from the James Webb Space Telescope")
+    (description
+     "This package provides an access to the JWST Science Calibration Pipeline
+processes data from all JWST instruments and observing modes by applying various
+science corrections sequentially, producing both fully-calibrated individual
+exposures and high-level data products (mosaics, extracted spectra, etc.).")
+    (license license:bsd-3)))
+
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-- 
2.40.1

Message #62 received at 63806 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 63806 <at> debbugs.gnu.org
Cc: efraim <at> flashner.co.il, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Date: Fri, 9 Jun 2023 10:33:25 +0200

[Message part 1 (text/plain, inline)]

Hi Guix!

Gentle ping here.

It's a brand new patch set, passed QA but might need any sort of
modification which I need to apply. Please, let me know if the review
revivals any issues.

Thanks,
Oleg

[Message part 2 (text/html, inline)]

Message #67 received at 63806-done <at> debbugs.gnu.org (full text, mbox):

From: Efraim Flashner <efraim <at> flashner.co.il>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 63806-done <at> debbugs.gnu.org, Eric Bavier <bavier <at> posteo.net>
Subject: Re: [bug#63806] [PATCH 00/18]: gnu: Add JWST (James Webb Space
 Telescope)
Date: Wed, 14 Jun 2023 14:59:14 +0300

[Message part 1 (text/plain, inline)]

Patches look good. I adjusted the line lengths a bit in the descriptions
but I think that's about it.

Patches pushed!

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   רנשלפ םירפא
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[signature.asc (application/pgp-signature, inline)]

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