fluiddyn issueshttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues2023-07-10T18:34:05Zhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/28CI: limit jobs to OSUOSL runners only2023-07-10T18:34:05ZMeisam TabrizCI: limit jobs to OSUOSL runners onlyDependency proxy on clever-cloud runners is intermittently failing! For example see [jobs/1990203](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990203), [jobs/1990365](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990365), [...Dependency proxy on clever-cloud runners is intermittently failing! For example see [jobs/1990203](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990203), [jobs/1990365](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990365), [jobs/1990448](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990448).
Heptapod server admins [are already aware of this issue](https://matrix.to/#/!UmEcDGVKKCwVOsunYF:matrix.org/$OLku_H38_nyKoq8ynHa5yst_BFh76D_UQ22rAjGFv7Y?via=matrix.org&via=integrations.ems.host&via=matrix4me.nl).https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/27fix python version incompatibilities/requirements2023-07-06T12:11:13ZMeisam Tabrizfix python version incompatibilities/requirementsThe minimum required python version for the project [is currently 3.8](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990993)!
```bash
fluiddyn/clusters/slurm.py
'subprocess.run(text)' requires 3.7
fluiddyn/util/compat.py
'func...The minimum required python version for the project [is currently 3.8](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1990993)!
```bash
fluiddyn/clusters/slurm.py
'subprocess.run(text)' requires 3.7
fluiddyn/util/compat.py
'functools.cached_property' member requires 3.8
```
Either fix the incompatibility or update the documentation to reflect this requirement. Add a CI test to enforce the documented minimum required python version.https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/26add missing test dependencies to CI container2023-07-13T14:26:55ZMeisam Tabrizadd missing test dependencies to CI containerfluiddyn.calcul.test.test_easypyfft.TestFFTWGrid (test_fftw_grid_size)
```
fluiddyn/calcul/test/test_easypyfft.py:31: fftw_grid_size depends on the package pulp, which is not installed.
```
fluiddyn.calcul.test.test_sphericalharmo.Test...fluiddyn.calcul.test.test_easypyfft.TestFFTWGrid (test_fftw_grid_size)
```
fluiddyn/calcul/test/test_easypyfft.py:31: fftw_grid_size depends on the package pulp, which is not installed.
```
fluiddyn.calcul.test.test_sphericalharmo.TestSphericalHarmo (test_sht_random)
```
fluiddyn/calcul/test/test_sphericalharmo.py:20: SHTns not installed or can not be imported.
```https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/25define target version for black2023-07-06T14:47:38ZMeisam Tabrizdefine target version for blackDepending on the python versions that should be supported by Black's output, the style of code may change. For example see the [results](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1984700) with [target-version = py36](https://fos...Depending on the python versions that should be supported by Black's output, the style of code may change. For example see the [results](https://foss.heptapod.net/fluiddyn/fluiddyn/-/jobs/1984700) with [target-version = py36](https://foss.heptapod.net/fluiddyn/fluiddyn/-/blob/f9126ac80035411cf63b996c438c7110fd324685/pyproject.toml#L49)https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/23Adopt a CoC2022-02-21T11:31:49ZPierre AugierAdopt a CoCI think we need to adopt a CoC.
See:
- the CoC adopted by foss.heptapod.net https://foss.heptapod.net/heptapod/foss.heptapod.net/-/issues/118 (inspired by Rust's CoC)
- https://scikit-image.org/docs/dev/conduct/code_of_conduct.html
...I think we need to adopt a CoC.
See:
- the CoC adopted by foss.heptapod.net https://foss.heptapod.net/heptapod/foss.heptapod.net/-/issues/118 (inspired by Rust's CoC)
- https://scikit-image.org/docs/dev/conduct/code_of_conduct.html
I tend to prefer something shorter as Rust CoC.Improve visibilityPierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/22Replace pkg_resources.resource_filename in fluiddoc.fluiddocset2022-02-21T11:56:54ZPierre AugierReplace pkg_resources.resource_filename in fluiddoc.fluiddocset`pkg_resources` is [provided by setuptools](https://setuptools.pypa.io/en/latest/pkg_resources.html).
We don't want to depend on setuptools at runtime. In the doc, it is mentioned "Use of pkg_resources is discouraged in favor of importl...`pkg_resources` is [provided by setuptools](https://setuptools.pypa.io/en/latest/pkg_resources.html).
We don't want to depend on setuptools at runtime. In the doc, it is mentioned "Use of pkg_resources is discouraged in favor of importlib.resources, importlib.metadata, and their backports (resources, metadata). Please consider using those libraries instead of pkg_resources."
However, I don't know yet how to replace our use of `pkg_resources.resource_filename` in https://foss.heptapod.net/fluiddyn/fluiddyn/-/blob/branch/default/fluiddoc/fluiddocset.py#L49.
```python
doc_src = Path(resource_filename(pkg_name, "/")).parent / "doc"
```https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/21Add CITATION.cff files2021-11-09T18:37:39ZAshwin V. MohananAdd CITATION.cff filesSaw this today at [xarray's repo](https://github.com/pydata/xarray/pull/5956). Supported by GitHub, Zenodo and Zotero. So it would be good to have.
- https://citation-file-format.github.io/
- https://docs.github.com/en/repositories/mana...Saw this today at [xarray's repo](https://github.com/pydata/xarray/pull/5956). Supported by GitHub, Zenodo and Zotero. So it would be good to have.
- https://citation-file-format.github.io/
- https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
Tools to generate them:
- https://citation-file-format.github.io/cff-initializer-javascript/#/
- https://github.com/citation-file-format/citation-file-format#tools-to-work-with-citationcff-files-wrench
- [ ] fluiddyn
- [ ] fluidfft
- [ ] fluidsimhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/20Fix inconsistency in fluiddyn.cluster2021-10-27T04:59:39ZPierre AugierFix inconsistency in fluiddyn.cluster[Here](https://github.com/exabl/snek5000/issues/61#issuecomment-951959814), I wrote:
> I think there is an inconsistency between different flavors of clusters in fluiddyn.clusters. It has to be fixed.
>
> For SLURM and PBS clusters, if ...[Here](https://github.com/exabl/snek5000/issues/61#issuecomment-951959814), I wrote:
> I think there is an inconsistency between different flavors of clusters in fluiddyn.clusters. It has to be fixed.
>
> For SLURM and PBS clusters, if nb_mpi_processes is not set (leading to nb_mpi_processes = None), the default value is nb_cores_per_node * nb_nodes. It is not the case for OAR clusters.
>
> We actually already use this behavior at LEGI to launch fluidimage processing without MPI.
I think we anyway need to "break the world" for at least some clusters. I tend to think the behavior we have for OAR is more reasonable and better (for fluidimage, snek5000, dask, etc.).
We could support `nb_mpi_processes="auto"` to specify that we want to launch a MPI command without explicitly computing the number `nb_mpi_processes`.
This way, it would be much simpler to launch snek5000 simulations on Slurm and PBS clusters.
@avmo would it be alright for you? I guess you would need to adapt some of your scripts...Pierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/19Doc about Windows2020-12-02T13:39:11ZPierre AugierDoc about WindowsWe could add few informations about how to setup a correct environment on Windows.
Example:
```json
[
{
// Make changes here to the powershell.exe profile.
"guid": "{61c54bbd-c2c6-5271-96e7-0...We could add few informations about how to setup a correct environment on Windows.
Example:
```json
[
{
// Make changes here to the powershell.exe profile.
"guid": "{61c54bbd-c2c6-5271-96e7-009a87ff44bf}",
"name": "Windows PowerShell",
"commandline": "powershell.exe",
"hidden": false
},
{
// Make changes here to the cmd.exe profile.
"guid": "{0caa0dad-35be-5f56-a8ff-afceeeaa6101}",
"name": "Invite de commandes",
"commandline": "cmd.exe",
"hidden": false
},
{
"guid": "{391a7fb7-cd0c-4800-909f-4f6680e79725}",
"name": "Anaconda PowerShell",
"commandline": "powershell.exe -ExecutionPolicy ByPass -NoExit -Command & '%USERPROFILE%\\miniconda3\\shell\\condabin\\conda-hook.ps1' ; conda activate '%USERPROFILE%\\miniconda3'",
"colorscheme": "Solarized Light",
"startingDirectory": "%USERPROFILE%",
"hidden": false
}
]
```Pierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/18Tests failed with h5py-openmpi2020-12-14T22:22:03ZAshwin V. MohananTests failed with h5py-openmpiSome test failures I noticed while building with system libraries in Arch Linux, which includes `python-h5py-openmpi`
```py
self = <fluiddyn.io.test.test_hdf5.TestHdf5 testMethod=test_functions>
def test_functions(self):
p...Some test failures I noticed while building with system libraries in Arch Linux, which includes `python-h5py-openmpi`
```py
self = <fluiddyn.io.test.test_hdf5.TestHdf5 testMethod=test_functions>
def test_functions(self):
path = "test_functions0.h5"
a = 1
b = "str"
c = np.ones(2)
d = 10
save_variables_h5(path, locals(), ("a", "b", "c"))
variables1 = load_variables_h5(path)
self.assertEqual(a, variables1["a"])
> self.assertEqual(b, variables1["b"])
E AssertionError: 'str' != b'str'
/home/avmo/.cache/aur/python-fluiddyn/src/fluiddyn-0.3.3/fluiddyn/io/test/test_hdf5.py:77: AssertionError
_____________________________________________________________________________ TestContainer.test_save_load_hdf5 _____________________________________________________________________________
self = <fluiddyn.util.test.test_paramcontainer.TestContainer testMethod=test_save_load_hdf5>
def test_save_load_hdf5(self):
"""Test save to and load from hdf5 file."""
params = self.params
name_file_h5 = "params_test.h5"
params._save_as_hdf5(path_file=name_file_h5)
params._save_as_hdf5()
params2 = ParamContainer(path_file=name_file_h5)
os.remove(name_file_h5)
try:
> self.assertEqual(self.params, params2)
/home/avmo/.cache/aur/python-fluiddyn/src/fluiddyn-0.3.3/fluiddyn/util/test/test_paramcontainer.py:85:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <fluiddyn.util.paramcontainer.ParamContainer object at 0x7fb3a3b9a550>
<params a0="1" a1="1" a2="a" a_str_list="['a', 'b']">
<child0 a0="[1]" a1="None">
<cc/>
</child0>
</params>
other = <fluiddyn.util.paramcontainer.ParamContainer object at 0x7fb3a3b9a580>
<params a0="1" a1="1" a2="a" a_str_list="array(['a', 'b'], dtype=object)">
<child0 a0="array([1])" a1="None">
<cc/>
</child0>
</params>
def __eq__(self, other):
> return self._make_dict() == other._make_dict()
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
/home/avmo/.cache/aur/python-fluiddyn/src/fluiddyn-0.3.3/fluiddyn/util/paramcontainer.py:392: ValueError
```Maintainencehttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/17crashed install on win8+py32020-11-20T21:11:18Zalexraynecrashed install on win8+py3Hallow!
work on win8 + python3.8
have instaled fluiddyn by pip install (as described here https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html)
and tortoiseHG shows this:
```
(venv.py38) D:\projects\hg\thg\thg.work>pytho...Hallow!
work on win8 + python3.8
have instaled fluiddyn by pip install (as described here https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html)
and tortoiseHG shows this:
```
(venv.py38) D:\projects\hg\thg\thg.work>python ./thg --nofork --debug --traceback
Traceback (most recent call last):
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\extensions.py", line 251, in _runuis
uisetup(ui)
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\hgfluiddyn\__init__.py", line 71, in uisetup
ui.warn(
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\ui.py", line 1753, in warn
self._writemsg(self._fmsgerr, type=b'warning', *msg, **opts)
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\ui.py", line 1235, in _writemsg
_writemsgwith(self._write, dest, *args, **opts)
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\ui.py", line 2368, in _writemsgwith
write(dest, *args, **opts)
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\ui.py", line 1178, in _write
self._writenobuf(dest, *args, **opts)
File "D:\projects\hg\thg\thg.work\venv.py38\lib\site-packages\mercurial\ui.py", line 1184, in _writenobuf
msg = b''.join(args)
TypeError: sequence item 0: expected a bytes-like object, str found
*** failed to set up extension hgfluiddyn: sequence item 0: expected a bytes-like object, str found
```https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/16Request an specific example2020-11-07T05:17:30Z汪梦真Request an specific exampleHello, I am a graduate student of Taiyuan University of technology. My recent research is related to your development software. I would like to ask if you have specific examples of using this software, if so, I hope you can reply to me a...Hello, I am a graduate student of Taiyuan University of technology. My recent research is related to your development software. I would like to ask if you have specific examples of using this software, if so, I hope you can reply to me as soon as possible, thank you.https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/15issue2020-11-06T08:02:55Z汪梦真issueHello, I am a graduate student. My recent research project is related to your software. Would you like to ask if you have specific examples of using this software, if you have, you can contact me through this email, thank you.Hello, I am a graduate student. My recent research project is related to your software. Would you like to ask if you have specific examples of using this software, if you have, you can contact me through this email, thank you.https://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/14Mirroring fluiddyn repositories to https://github.com/fluiddyn/2020-10-06T12:44:43ZPierre AugierMirroring fluiddyn repositories to https://github.com/fluiddyn/It works for https://foss.heptapod.net/graphics/plot-covid19-fr/-/settings/repository so it is doable.
- [x] fluiddyn
- [x] transonic
- [x] fluidfft
- [x] fluidsim
- [x] fluidimage
- [x] fluidlab
- [x] fluidshtIt works for https://foss.heptapod.net/graphics/plot-covid19-fr/-/settings/repository so it is doable.
- [x] fluiddyn
- [x] transonic
- [x] fluidfft
- [x] fluidsim
- [x] fluidimage
- [x] fluidlab
- [x] fluidshtPierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/13Use MyST anq fix the doc (links in notebooks)2022-02-05T21:10:54ZPierre AugierUse MyST anq fix the doc (links in notebooks)Use MyST-NB (https://myst-nb.readthedocs.io):
- [x] fluiddyn
- [ ] fluidfft
- [x] fluidsim
- [ ] fluidlab
- [ ] fluidimage
- [ ] fluidsht
See for example https://fluiddyn.readthedocs.io/en/latest/ipynb/overview.htmlUse MyST-NB (https://myst-nb.readthedocs.io):
- [x] fluiddyn
- [ ] fluidfft
- [x] fluidsim
- [ ] fluidlab
- [ ] fluidimage
- [ ] fluidsht
See for example https://fluiddyn.readthedocs.io/en/latest/ipynb/overview.htmlPierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/12Changelog and communication2024-01-10T19:43:16ZAshwin V. MohananChangelog and communicationSince now only occasionally involved in the project, I notice something that could improve the overall project health of FluidDyn.
# The good
With the merge request based workflow, things are a bit more cohesive than it used to be. Tha...Since now only occasionally involved in the project, I notice something that could improve the overall project health of FluidDyn.
# The good
With the merge request based workflow, things are a bit more cohesive than it used to be. Thanks to Heptapod, I can follow the development via this page: https://foss.heptapod.net/groups/fluiddyn/-/activity. :100:
# The bad
Changelog for some recent releases are too short. See fluidfft 0.3.1 and transonic 0.4.3 for instance, which is a variation of "various bug fixes". It does not help the reader. :confused:
# What can change
Project maintainance is a tough job already. I understand. But one could produce better changelogs. Some solutions
1. [`towncrier`](https://github.com/twisted/towncrier) is a package which assists developers in this regard. I have not used it personally, but [looks like NumPy has adopted it](https://github.com/numpy/numpy/blob/99010006fabea949d13aae8caea10abf97cbaed9/pyproject.toml#L10-L71).
2. [Keep a changelog](https://keepachangelog.com/en/1.0.0/) has a nice template for clearly defining what has changed. It also helps in deciding whether the next release would be a major / minor / patch release.
Once this improved changelog is ready and a new version is out, send it out to the mailing list. Then, tweet the link to the mailing list archive so that others know about it.
# To Do
- [x] fluidsim
- [ ] fluidfft
- [ ] fluidimage
- [ ] fluidlab
# pyproject.toml pending
- [ ] fluidsht
- [ ] transonicMaintainenceAshwin V. MohananAshwin V. Mohananhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/11Isolated builds and pyproject.toml (PEP 517/518)2020-10-12T13:48:16ZPierre AugierIsolated builds and pyproject.toml (PEP 517/518)See
- https://discuss.python.org/t/options-to-build-the-same-package-in-different-ways-with-different-build-dependencies/4458
- https://www.python.org/dev/peps/pep-0517/
- https://www.python.org/dev/peps/pep-0518/
- https://snarky.ca/w...See
- https://discuss.python.org/t/options-to-build-the-same-package-in-different-ways-with-different-build-dependencies/4458
- https://www.python.org/dev/peps/pep-0517/
- https://www.python.org/dev/peps/pep-0518/
- https://snarky.ca/what-the-heck-is-pyproject-toml/Pierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/10Release fluiddyn 0.3.22020-03-31T11:19:12ZPierre AugierRelease fluiddyn 0.3.2I'd like to release a new version of fluiddyn very soon.
First, this needs to be done:
- [x] fix #9 (Update cluster LEGI)
Other things that can be useful to put in this version?I'd like to release a new version of fluiddyn very soon.
First, this needs to be done:
- [x] fix #9 (Update cluster LEGI)
Other things that can be useful to put in this version?Pierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/9Update clusters LEGI2020-03-31T09:29:18ZPierre AugierUpdate clusters LEGII think there is now another cluster called Cluster2 at LEGI.
@ClementS and @jreneuve can you please confirm?I think there is now another cluster called Cluster2 at LEGI.
@ClementS and @jreneuve can you please confirm?Pierre AugierPierre Augierhttps://foss.heptapod.net/fluiddyn/fluiddyn/-/issues/8Setup CI with Heptapod for some repositories2020-09-24T07:56:33ZPierre AugierSetup CI with Heptapod for some repositoriesWe need to add .gitlab-ci.yml (also add CODECOV_TOKEN).
* [x] fluiddyn
* [x] transonic
* [x] fluidsim
* [x] fluidfft
* [x] fluidsht
* [x] fluidimage
* [x] fluidlab
See https://foss.heptapod.net/fluiddyn/fluiddyn/blob/branch/default/.gi...We need to add .gitlab-ci.yml (also add CODECOV_TOKEN).
* [x] fluiddyn
* [x] transonic
* [x] fluidsim
* [x] fluidfft
* [x] fluidsht
* [x] fluidimage
* [x] fluidlab
See https://foss.heptapod.net/fluiddyn/fluiddyn/blob/branch/default/.gitlab-ci.ymlPierre AugierPierre Augier