GNU bug report logs -
#54869
[PATCH 0/5] gnu: python-vedo: Update to 2022.2.0 and sanity-check failures.
Previous Next
To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 54869 in the body.
You can then email your comments to 54869 AT debbugs.gnu.org in the normal way.
Toggle the display of automated, internal messages from the tracker.
Report forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Tue, 12 Apr 2022 01:23:02 GMT)
Full text and
rfc822 format available.
Acknowledgement sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
New bug report received and forwarded. Copy sent to
guix-patches <at> gnu.org
.
(Tue, 12 Apr 2022 01:23:02 GMT)
Full text and
rfc822 format available.
Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
Hello,
The following patch series updates python-vedo to its latest version,
and also adds support for the #:tests? flag to fenics-dolfin, fenics and
python-vedo.
Unfortunately, I can't get fenics or python-vedo to build except by
deleting the sanity-check phase, and this even before applying any of my
patches.
(I've confirmed that my patches are correct by testing the builds
without sanity-checks, so applying them shouldn't be an issue.)
The following is the sanity-check error obtained when building fenics:
starting phase `sanity-check'
validating 'fenics-dolfin' /gnu/store/lkb8mx8dk82znkzfgnx1k1mklaj9b34d-fenics-2019.1.0.post0/lib/python3.9/site-packages
...checking requirements: ERROR: fenics-dolfin==2019.1.0 ContextualVersionConflict(pybind11 2.8.1 (/gnu/store/qmxw9dqqywrlllzlidv09f2nazirjwk7-pybind11-2.8.1/lib/python3.9/site-packages), Requirement.parse('pybind11==2.2.4'), {'fenics-dolfin'})
error: in phase 'sanity-check': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/lkb8mx8dk82znkzfgnx1k1mklaj9b34d-fenics-2019.1.0.post0/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>
phase `sanity-check' failed after 0.2 seconds
Note that it complains that pybind11 is not at version 2.2.4, but when
fenics was last updated (in commit 37bb0d1eafb3f08a204aed8c928cbf7cbc69cd19),
the version of pybind11 at the time was 2.3.0, so this would appear to
be either a new issue, or an issue specific to my machine (foreign distro).
The sanity-check errors from vedo are similarly bizarre -- they complain
about a missing vtk, but it is there in the propagated inputs.
With old version of python-vedo:
starting phase `sanity-check'
validating 'vedo' /gnu/store/4h10widg2y0nhvacz8mricn187qzw9dq-python-vedo-2021.0.3/lib/python3.9/site-packages
...checking requirements: ERROR: vedo==2021.0.3 DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
error: in phase 'sanity-check': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/4h10widg2y0nhvacz8mricn187qzw9dq-python-vedo-2021.0.3/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>
phase `sanity-check' failed after 0.2 seconds
With updated version of python-vedo (i.e., including the
python-deprecated propagated input):
starting phase `sanity-check'
validating 'vedo' /gnu/store/a6g20gkvi1l70arh2rm53x7gm30dzqcp-python-vedo-2022.2.0/lib/python3.9/site-packages
...checking requirements: ERROR: vedo==2022.2.0 DistributionNotFound(Requirement.parse('vtk<9.1.0'), {'vedo'})
error: in phase 'sanity-check': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/a6g20gkvi1l70arh2rm53x7gm30dzqcp-python-vedo-2022.2.0/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>
phase `sanity-check' failed after 0.2 seconds
The latest commit of fenics (there isn't a newer release than the one
included in Guix) no longer requires a specific version of pybind11 [1],
and in addition, it seems the focus is on the dolfinx project [2] rather
than dolfin (dolfin is already considered legacy [3]), so perhaps it
would be worth updating the fenics package to the latest git commit.
That wouldn't solve the problem python-vedo's sanity-check is
encountering, though.
Any help would be appreciated.
Best regards,
Paul
[1]: https://bitbucket.org/fenics-project/dolfin/src/d29e24d19eab5200a55e43a3e18e1f38214fb5a8/python/setup.py#lines-22)
[2]: https://github.com/FEniCS/dolfinx
[3]: https://fenicsproject.org/
Paul A. Patience (5):
gnu: fenics-dolfin: Honor #:tests? flag.
gnu: fenics: Honor #:tests? flag.
gnu: python-vedo: Honor #:tests? flag.
gnu: python-vedo: Remove input labels.
gnu: python-vedo: Update to 2022.2.0.
gnu/packages/python-science.scm | 35 ++++++++++++++++----------------
gnu/packages/simulation.scm | 36 +++++++++++++++++----------------
2 files changed, 37 insertions(+), 34 deletions(-)
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:01 GMT)
Full text and
rfc822 format available.
Message #10 received at 54869 <at> debbugs.gnu.org (full text, mbox):
I've fixed the sanity check issues in this patch series, along with some other
minor things (particularly in the python-vedo package).
There is still one problem, though, but it has been present (for me) since
before any of these patches: one of the fenics tests around 24 % of the test
suite hangs.
I have to build it with --without-tests=fenics, but since it was present since
before, I haven't disabled the tests in the fenics package.
Oh, also, I tried to remove the input labels from fenics-dolfin, but ran into
build errors (failing to find catch.cpp).
Paul A. Patience (7):
gnu: fenics-dolfin: Honor #:tests? flag.
gnu: fenics: Honor #:tests? flag.
gnu: fenics: Fix sanity check.
gnu: python-vedo: Honor #:tests? flag.
gnu: python-vedo: Remove input labels.
gnu: python-vedo: Disable sanity check.
gnu: python-vedo: Update to 2022.2.0.
gnu/packages/python-science.scm | 57 ++++++++++++++++++++-------------
gnu/packages/simulation.scm | 40 +++++++++++++----------
2 files changed, 58 insertions(+), 39 deletions(-)
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:02 GMT)
Full text and
rfc822 format available.
Message #13 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics-dolfin)[arguments]: Adjust custom
'check' phase to honor the #:tests? flag.
---
gnu/packages/simulation.scm | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3f2d8e136d..aebb6be15e 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -549,12 +549,13 @@ (define-public fenics-dolfin
")\n") port)))
#t))
(replace 'check
- (lambda _
- (and (invoke "make" "unittests")
- (invoke "make" "demos")
- (invoke "ctest" "-R" "unittests")
- (invoke "ctest" "-R" "demo" "-R" "serial")
- (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (and (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi"))))))))
(home-page "https://bitbucket.org/fenics-project/dolfin/")
(synopsis "Problem solving environment for differential equations")
(description
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:02 GMT)
Full text and
rfc822 format available.
Message #16 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics)[arguments]: Adjust custom 'check'
phase to honor the #:tests? flag.
---
gnu/packages/simulation.scm | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index aebb6be15e..3260841608 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -660,17 +660,18 @@ (define-public fenics
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
(setenv "OPENBLAS_NUM_THREADS" "1")))
(replace 'check
- (lambda _
- (with-directory-excursion "test"
- ;; Note: The test test_snes_set_from_options() in the file
- ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- ;; Limit the number of jobs to 3 as 500 MiB of memory is used
- ;; per process.
- (invoke "mpirun" "-np" (number->string
- (min 3 (parallel-job-count)))
- "python" "-B" "-m"
- "pytest" "unit" "--ignore"
- "unit/nls/test_PETScSNES_solver.py"))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test"
+ ;; Note: The test test_snes_set_from_options() in the file
+ ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+ ;; Limit the number of jobs to 3 as 500 MiB of memory is used
+ ;; per process.
+ (invoke "mpirun" "-np" (number->string
+ (min 3 (parallel-job-count)))
+ "python" "-B" "-m"
+ "pytest" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py")))))
(add-after 'install 'install-demo-files
(lambda* (#:key outputs #:allow-other-keys)
(let* ((demos (string-append
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:02 GMT)
Full text and
rfc822 format available.
Message #19 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics)[arguments]: Relax pybind11
requirement to appease the sanity check.
---
gnu/packages/simulation.scm | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3260841608..b0f6046022 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -610,6 +610,10 @@ (define-public fenics
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("pybind11==") "pybind11>="))))
(add-after 'patch-source-shebangs 'set-paths
(lambda _
;; Define paths to store locations.
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:03 GMT)
Full text and
rfc822 format available.
Message #22 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[arguments]: Adjust
custom 'check' phase to honor the #:tests? flag. Also remove its
trailing boolean.
---
gnu/packages/python-science.scm | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 07d713e013..4538904b68 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -876,15 +876,15 @@ (define-public python-vedo
(add-after 'build 'mpi-setup
,%openmpi-setup)
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (setenv "HOME" (getcwd))
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "tests"
- (for-each (lambda (dir)
- (with-directory-excursion dir
- (invoke "./run_all.sh")))
- '("common" "dolfin")))
- #t)))))
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" (getcwd))
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "tests"
+ (for-each (lambda (dir)
+ (with-directory-excursion dir
+ (invoke "./run_all.sh")))
+ '("common" "dolfin")))))))))
(inputs ; for the check phase
`(("dolfin" ,fenics)
("pkgconfig" ,python-pkgconfig)
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:03 GMT)
Full text and
rfc822 format available.
Message #25 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable
sanity check.
---
gnu/packages/python-science.scm | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3afaa0efc2..d0fca49aaf 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -884,7 +884,13 @@ (define-public python-vedo
(for-each (lambda (dir)
(with-directory-excursion dir
(invoke "./run_all.sh")))
- '("common" "dolfin")))))))))
+ '("common" "dolfin"))))))
+ ;; Disable the sanity check, which fails with the following error:
+ ;;
+ ;; ...checking requirements: ERROR: vedo==2021.0.3 DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
+ ;;
+ ;; Probably it cannot find VTK because it isn't a Python library.
+ (delete 'sanity-check))))
(inputs ; for the check phase
(list fenics
python-matplotlib
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:04 GMT)
Full text and
rfc822 format available.
Message #28 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[inputs]: Remove labels
and sort the inputs.
[propagated-inputs]: Remove labels.
---
gnu/packages/python-science.scm | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4538904b68..3afaa0efc2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -886,14 +886,14 @@ (define-public python-vedo
(invoke "./run_all.sh")))
'("common" "dolfin")))))))))
(inputs ; for the check phase
- `(("dolfin" ,fenics)
- ("pkgconfig" ,python-pkgconfig)
- ("matplotlib" ,python-matplotlib)))
+ (list fenics
+ python-matplotlib
+ python-pkgconfig))
(native-inputs ; for python-pkgconfig
(list pkg-config))
(propagated-inputs
- `(("numpy" ,python-numpy)
- ("vtk" ,vtk)))
+ (list python-numpy
+ vtk))
(home-page "https://github.com/marcomusy/vedo")
(synopsis
"Analysis and visualization of 3D objects and point clouds")
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 11:54:04 GMT)
Full text and
rfc822 format available.
Message #31 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo): Update to 2022.2.0.
[arguments]: Add 'fix-tests' phase.
[inputs]: Move fenics and python-matplotlib to propagated-inputs.
Move python-pkgconfig from here...
[native-inputs]: ...to here.
[propagated-inputs]: Add python-deprecated (and fenics and
python-matplotlib).
[description]: Make description more accurate.
---
gnu/packages/python-science.scm | 31 +++++++++++++++++++------------
1 file changed, 19 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d0fca49aaf..b1fc94cecc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -17,6 +17,7 @@
;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
;;; Copyright © 2022 Guillaume Le Vaillant <glv <at> posteo.net>
+;;; Copyright © 2022 Paul A. Patience <paul <at> apatience.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -858,21 +859,28 @@ (define-public python-upsetplot
(define-public python-vedo
(package
(name "python-vedo")
- (version "2021.0.3")
+ (version "2022.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/marcomusy/vedo")
- (commit version)))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "18i3ajh5jzhpc86di15lwh4jv97jhm627ii877sa4yhv6abzjfpn"))))
+ "1hhv4xc4bphhd1zrnf7r6fpf65xvkdqmb1lh51qg1xpv91h2az0h"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ ;; These tests require online data.
+ (lambda _
+ (substitute* "tests/common/test_actors.py"
+ (("^st = .*") "")
+ (("^assert isinstance\\(st\\.GetTexture\\(\\), .*") ""))
+ (delete-file "tests/common/test_pyplot.py")))
(add-after 'build 'mpi-setup
,%openmpi-setup)
(replace 'check
@@ -887,18 +895,18 @@ (define-public python-vedo
'("common" "dolfin"))))))
;; Disable the sanity check, which fails with the following error:
;;
- ;; ...checking requirements: ERROR: vedo==2021.0.3 DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
+ ;; ...checking requirements: ERROR: vedo==2022.2.0 DistributionNotFound(Requirement.parse('vtk<9.1.0'), {'vedo'})
;;
;; Probably it cannot find VTK because it isn't a Python library.
(delete 'sanity-check))))
- (inputs ; for the check phase
- (list fenics
- python-matplotlib
+ (native-inputs
+ (list pkg-config
python-pkgconfig))
- (native-inputs ; for python-pkgconfig
- (list pkg-config))
(propagated-inputs
- (list python-numpy
+ (list fenics
+ python-deprecated
+ python-matplotlib
+ python-numpy
vtk))
(home-page "https://github.com/marcomusy/vedo")
(synopsis
@@ -909,8 +917,7 @@ (define-public python-vedo
range of functionalities for working with three-dimensional meshes and
point clouds. It can also be used to generate high quality
two-dimensional renderings such as scatter plots and histograms.
-@code{vedo} is based on @code{vtk} and @code{numpy}, with no other
-dependencies.")
+@code{vedo} is based on @code{vtk} and @code{numpy}.")
;; vedo is released under the Expat license. Included fonts are
;; covered by the OFL license and textures by the CC0 license.
;; The earth images are in the public domain.
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 17:48:02 GMT)
Full text and
rfc822 format available.
Message #34 received at 54869 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Paul A. Patience schreef op vr 22-04-2022 om 11:53 [+0000]:
> - (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
> + (lambda* (#:key tests? #:allow-other-keys)
> + (when tests?
> + (and (invoke "make" "unittests")
> + (invoke "make" "demos")
> + (invoke "ctest" "-R" "unittests")
> + (invoke "ctest" "-R" "demo" "-R" "serial")
> + (invoke "ctest" "-R" "demo" "-R" "mpi"))))))))
The 'and' is pointless, it can be removed --- IIUC, 'invoke' throws
exceptions, it doesn't return #false. Anyway, honouring #:tests? is
nice (for cross-compilation and --without-tests=...).
Greetings,
Maxime.
[signature.asc (application/pgp-signature, inline)]
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:26:01 GMT)
Full text and
rfc822 format available.
Message #37 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics)[arguments]: Adjust custom 'check'
phase to honor the #:tests? flag.
---
gnu/packages/simulation.scm | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 757738e627..230ae62826 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -657,17 +657,18 @@ (define-public fenics
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
(setenv "OPENBLAS_NUM_THREADS" "1")))
(replace 'check
- (lambda _
- (with-directory-excursion "test"
- ;; Note: The test test_snes_set_from_options() in the file
- ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- ;; Limit the number of jobs to 3 as 500 MiB of memory is used
- ;; per process.
- (invoke "mpirun" "-np" (number->string
- (min 3 (parallel-job-count)))
- "python" "-B" "-m"
- "pytest" "unit" "--ignore"
- "unit/nls/test_PETScSNES_solver.py"))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test"
+ ;; Note: The test test_snes_set_from_options() in the file
+ ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+ ;; Limit the number of jobs to 3 as 500 MiB of memory is used
+ ;; per process.
+ (invoke "mpirun" "-np" (number->string
+ (min 3 (parallel-job-count)))
+ "python" "-B" "-m"
+ "pytest" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py")))))
(add-after 'install 'install-demo-files
(lambda* (#:key outputs #:allow-other-keys)
(let* ((demos (string-append
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:26:02 GMT)
Full text and
rfc822 format available.
Message #40 received at 54869 <at> debbugs.gnu.org (full text, mbox):
I've integrated the suggestions of Maxime Devos.
Paul A. Patience (7):
gnu: fenics-dolfin: Honor #:tests? flag.
gnu: fenics: Honor #:tests? flag.
gnu: fenics: Fix sanity check.
gnu: python-vedo: Honor #:tests? flag.
gnu: python-vedo: Remove input labels.
gnu: python-vedo: Disable sanity check.
gnu: python-vedo: Update to 2022.2.0.
gnu/packages/python-science.scm | 55 ++++++++++++++++++++-------------
gnu/packages/simulation.scm | 49 +++++++++++++++--------------
2 files changed, 59 insertions(+), 45 deletions(-)
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:02 GMT)
Full text and
rfc822 format available.
Message #43 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics)[arguments]: Relax pybind11
requirement to appease the sanity check.
---
gnu/packages/simulation.scm | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 230ae62826..b15743f747 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -607,6 +607,10 @@ (define-public fenics
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("pybind11==") "pybind11>="))))
(add-after 'patch-source-shebangs 'set-paths
(lambda _
;; Define paths to store locations.
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:02 GMT)
Full text and
rfc822 format available.
Message #46 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/simulation.scm (fenics-dolfin)[source]: Remove trailing
boolean.
[arguments]: Adjust custom 'check' phase to honor the #:tests? flag. While
here, remove trailing booleans.
---
gnu/packages/simulation.scm | 22 ++++++++++------------
1 file changed, 10 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3f2d8e136d..757738e627 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -448,8 +448,7 @@ (define-public fenics-dolfin
;; Specify directory to find the header file.
(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
(string-append front
- "$ENV{CATCH_DIR}/include" back "\n")))
- #t))))
+ "$ENV{CATCH_DIR}/include" back "\n")))))))
(build-system cmake-build-system)
(inputs
`(("blas" ,openblas)
@@ -494,8 +493,7 @@ (define-public fenics-dolfin
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
(setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
(setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
- (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
- #t))
+ (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))))
(add-before 'check 'pre-check
(lambda _
;; The Dolfin repository uses git-lfs, whereby web links are
@@ -546,15 +544,15 @@ (define-public fenics-dolfin
"demo_mesh-quality_serial "
"demo_mesh-quality_mpi "
"demo_multimesh-stokes_serial "
- ")\n") port)))
- #t))
+ ")\n") port)))))
(replace 'check
- (lambda _
- (and (invoke "make" "unittests")
- (invoke "make" "demos")
- (invoke "ctest" "-R" "unittests")
- (invoke "ctest" "-R" "demo" "-R" "serial")
- (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
(home-page "https://bitbucket.org/fenics-project/dolfin/")
(synopsis "Problem solving environment for differential equations")
(description
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:03 GMT)
Full text and
rfc822 format available.
Message #49 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[arguments]: Adjust
custom 'check' phase to honor the #:tests? flag. Also remove its
trailing boolean.
---
gnu/packages/python-science.scm | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 07d713e013..4538904b68 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -876,15 +876,15 @@ (define-public python-vedo
(add-after 'build 'mpi-setup
,%openmpi-setup)
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (setenv "HOME" (getcwd))
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "tests"
- (for-each (lambda (dir)
- (with-directory-excursion dir
- (invoke "./run_all.sh")))
- '("common" "dolfin")))
- #t)))))
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" (getcwd))
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "tests"
+ (for-each (lambda (dir)
+ (with-directory-excursion dir
+ (invoke "./run_all.sh")))
+ '("common" "dolfin")))))))))
(inputs ; for the check phase
`(("dolfin" ,fenics)
("pkgconfig" ,python-pkgconfig)
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:03 GMT)
Full text and
rfc822 format available.
Message #52 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[inputs]: Remove labels
and sort the inputs.
[propagated-inputs]: Remove labels.
---
gnu/packages/python-science.scm | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4538904b68..3afaa0efc2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -886,14 +886,14 @@ (define-public python-vedo
(invoke "./run_all.sh")))
'("common" "dolfin")))))))))
(inputs ; for the check phase
- `(("dolfin" ,fenics)
- ("pkgconfig" ,python-pkgconfig)
- ("matplotlib" ,python-matplotlib)))
+ (list fenics
+ python-matplotlib
+ python-pkgconfig))
(native-inputs ; for python-pkgconfig
(list pkg-config))
(propagated-inputs
- `(("numpy" ,python-numpy)
- ("vtk" ,vtk)))
+ (list python-numpy
+ vtk))
(home-page "https://github.com/marcomusy/vedo")
(synopsis
"Analysis and visualization of 3D objects and point clouds")
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:03 GMT)
Full text and
rfc822 format available.
Message #55 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable
sanity check.
---
gnu/packages/python-science.scm | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3afaa0efc2..676ca6474e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -884,7 +884,11 @@ (define-public python-vedo
(for-each (lambda (dir)
(with-directory-excursion dir
(invoke "./run_all.sh")))
- '("common" "dolfin")))))))))
+ '("common" "dolfin"))))))
+ ;; Disable the sanity check, which fails with the following error:
+ ;;
+ ;; ...checking requirements: ERROR: vedo==2021.0.3 DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
+ (delete 'sanity-check))))
(inputs ; for the check phase
(list fenics
python-matplotlib
--
2.35.1
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 22 Apr 2022 20:27:04 GMT)
Full text and
rfc822 format available.
Message #58 received at 54869 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/python-science.scm (python-vedo): Update to 2022.2.0.
[arguments]: Add 'fix-tests' phase.
[inputs]: Move fenics and python-matplotlib to propagated-inputs.
Move python-pkgconfig from here...
[native-inputs]: ...to here.
[propagated-inputs]: Add python-deprecated (and fenics and
python-matplotlib).
[description]: Make description more accurate.
---
gnu/packages/python-science.scm | 31 +++++++++++++++++++------------
1 file changed, 19 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 676ca6474e..ab307e31af 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -17,6 +17,7 @@
;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
;;; Copyright © 2022 Guillaume Le Vaillant <glv <at> posteo.net>
+;;; Copyright © 2022 Paul A. Patience <paul <at> apatience.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -858,21 +859,28 @@ (define-public python-upsetplot
(define-public python-vedo
(package
(name "python-vedo")
- (version "2021.0.3")
+ (version "2022.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/marcomusy/vedo")
- (commit version)))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "18i3ajh5jzhpc86di15lwh4jv97jhm627ii877sa4yhv6abzjfpn"))))
+ "1hhv4xc4bphhd1zrnf7r6fpf65xvkdqmb1lh51qg1xpv91h2az0h"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ ;; These tests require online data.
+ (lambda _
+ (substitute* "tests/common/test_actors.py"
+ (("^st = .*") "")
+ (("^assert isinstance\\(st\\.GetTexture\\(\\), .*") ""))
+ (delete-file "tests/common/test_pyplot.py")))
(add-after 'build 'mpi-setup
,%openmpi-setup)
(replace 'check
@@ -887,16 +895,16 @@ (define-public python-vedo
'("common" "dolfin"))))))
;; Disable the sanity check, which fails with the following error:
;;
- ;; ...checking requirements: ERROR: vedo==2021.0.3 DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
+ ;; ...checking requirements: ERROR: vedo==2022.2.0 DistributionNotFound(Requirement.parse('vtk<9.1.0'), {'vedo'})
(delete 'sanity-check))))
- (inputs ; for the check phase
- (list fenics
- python-matplotlib
+ (native-inputs
+ (list pkg-config
python-pkgconfig))
- (native-inputs ; for python-pkgconfig
- (list pkg-config))
(propagated-inputs
- (list python-numpy
+ (list fenics
+ python-deprecated
+ python-matplotlib
+ python-numpy
vtk))
(home-page "https://github.com/marcomusy/vedo")
(synopsis
@@ -907,8 +915,7 @@ (define-public python-vedo
range of functionalities for working with three-dimensional meshes and
point clouds. It can also be used to generate high quality
two-dimensional renderings such as scatter plots and histograms.
-@code{vedo} is based on @code{vtk} and @code{numpy}, with no other
-dependencies.")
+@code{vedo} is based on @code{vtk} and @code{numpy}.")
;; vedo is released under the Expat license. Included fonts are
;; covered by the OFL license and textures by the CC0 license.
;; The earth images are in the public domain.
--
2.35.1
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:01 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Message #63 received at 54869-done <at> debbugs.gnu.org (full text, mbox):
Hi Paul,
"Paul A. Patience" <paul <at> apatience.com> skribis:
> gnu: fenics-dolfin: Honor #:tests? flag.
> gnu: fenics: Honor #:tests? flag.
> gnu: fenics: Fix sanity check.
> gnu: python-vedo: Honor #:tests? flag.
> gnu: python-vedo: Remove input labels.
> gnu: python-vedo: Disable sanity check.
> gnu: python-vedo: Update to 2022.2.0.
Finally applied. Thank you, and thanks Maxime for reviewing!
Ludo’.
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:02 GMT)
Full text and
rfc822 format available.
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:03 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:03 GMT)
Full text and
rfc822 format available.
Reply sent
to
Ludovic Courtès <ludo <at> gnu.org>
:
You have taken responsibility.
(Fri, 06 May 2022 13:12:03 GMT)
Full text and
rfc822 format available.
Notification sent
to
"Paul A. Patience" <paul <at> apatience.com>
:
bug acknowledged by developer.
(Fri, 06 May 2022 13:12:03 GMT)
Full text and
rfc822 format available.
Information forwarded
to
guix-patches <at> gnu.org
:
bug#54869
; Package
guix-patches
.
(Fri, 06 May 2022 13:37:02 GMT)
Full text and
rfc822 format available.
Message #91 received at 54869-done <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Ludovic Courtès schreef op vr 06-05-2022 om 15:11 [+0200]:
> Finally applied. Thank you, and thanks Maxime for reviewing!
TBC I only looked rather superficially at things, I haven't build any
of the packages myself or looked into the source code of the packages.
Greetings,
Maxime.
[signature.asc (application/pgp-signature, inline)]
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Sat, 04 Jun 2022 11:24:08 GMT)
Full text and
rfc822 format available.
This bug report was last modified 1 year and 327 days ago.
Previous Next
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.