[PATCH 0/5] gnu: python-vedo: Update to 2022.2.0 and sanity-check failures.

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

merge 54869 54870 54871 54872 54873 54874

thanks

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

'check' phase to honor the #:tests? flag.

---

gnu/packages/simulation.scm | 13 +++++++------

1 file changed, 7 insertions(+), 6 deletions(-)

--

2.35.1

phase to honor the #:tests? flag.

---

gnu/packages/simulation.scm | 23 ++++++++++++-----------

1 file changed, 12 insertions(+), 11 deletions(-)

--

2.35.1

requirement to appease the sanity check.

---

gnu/packages/simulation.scm | 4 ++++

1 file changed, 4 insertions(+)

--

2.35.1

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(-)

--

2.35.1

sanity check.

---

gnu/packages/python-science.scm | 8 +++++++-

1 file changed, 7 insertions(+), 1 deletion(-)

--

2.35.1

and sort the inputs.

[propagated-inputs]: Remove labels.

---

gnu/packages/python-science.scm | 10 +++++-----

1 file changed, 5 insertions(+), 5 deletions(-)

--

2.35.1

[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(-)

--

2.35.1

Paul A. Patience schreef op vr 22-04-2022 om 11:53 [+0000]:

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.

phase to honor the #:tests? flag.

---

gnu/packages/simulation.scm | 23 ++++++++++++-----------

1 file changed, 12 insertions(+), 11 deletions(-)

--

2.35.1

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

requirement to appease the sanity check.

---

gnu/packages/simulation.scm | 4 ++++

1 file changed, 4 insertions(+)

--

2.35.1

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(-)

--

2.35.1

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(-)

--

2.35.1

and sort the inputs.

[propagated-inputs]: Remove labels.

---

gnu/packages/python-science.scm | 10 +++++-----

1 file changed, 5 insertions(+), 5 deletions(-)

--

2.35.1

sanity check.

---

gnu/packages/python-science.scm | 6 +++++-

1 file changed, 5 insertions(+), 1 deletion(-)

--

2.35.1

[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(-)

--

2.35.1

Hi Paul,

"Paul A. Patience" <paul@apatience.com> skribis:

Finally applied. Thank you, and thanks Maxime for reviewing!

Ludo’.

Ludovic Courtès schreef op vr 06-05-2022 om 15:11 [+0200]:

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.