pyOpenSci
Fluidimage submission
Submitting Author: Pierre Augier (@paugier) All current maintainers: (@paugier) Package Name: Fluidimage One-Line Description of Package: "Fluidimage: a Python framework to study flows from images" Repository Link: https://foss.heptapod.net/fluiddyn/fluidimage Version submitted: 0.5.3 EIC: @Batalex Editor: @cmarmo Reviewer 1: @leahmendelson Reviewer 2: @Kai-Striega Reviewer 3: @emmylia321 Archive: TBD JOSS DOI: TBD Version accepted: TBD Date accepted (month/day/year): TBD
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Description
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FluidImage is a free and open-source Python framework to process images of fluids (in particular with PIV), and analyse the resulting fields.
Fluidimage has now grown into a clean software reimplementing in modern Python algorithms and ideas taken from UVmat, OpenPIV, PIVlab and PIVmat with a focus on performance, usability and maintanability. However, Fluidimage is not restricted to Particle Image Velocimetry computations (PIV, i.e. displacements of pattern obtained by correlations of cropped images) and can be used to (i) display and pre-process images, (ii) compute displacement or velocity fields with PIV, Background-Oriented Schlieren (BOS) and optical flow, and (iii) analyze and display vector and scalar fields.
Scope
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Who is the target audience and what are scientific applications of this package?
The target audience is students, scientists, researchers and engineers working with images of fluids. Fluidimage can be used to process images, compute vectors and scalar fields and analyze them.
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Are there other Python packages that accomplish the same thing? If so, how does yours differ?
OpenPIV can be used to compute vectors with various PIV algorithms. Fluidimage is not restricted to PIV. It has a very different API than OpenPIV. Fluidimage has more focus on performance, with in particular compiled extensions produced with Transonic-Pythran and an asynchronous/parallel framework to describe "topologies" of computations and compute then in parallel.
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Publication Options
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I tend to think that Fluidimage is not yet ready for a paper in JOSS. We need more time to get a stronger community and to implement few more features before submitting to JOSS.
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- [x] Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.
Note that Fluidimage development is done on https://foss.heptapod.net/fluiddyn/fluidimage and that issues have to be filled on this website. Pull requests are of course very welcome. Note that with Heptapod/Mercurial, one should not fork the repo to submit a PR (see https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html).
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Editor comments
Hello @paugier, and welcome to pyOpenSci! Sorry it took me so long to get back to you, I have been sitting on these checks for a while now.
fluidimage is truly an interesting project, even from a code structure perspective. I never used mercurial, and I think it's a first for pyOpenSci in general. Same for the licence, never encountered it before!
I'll get started on finding an editor. Thank you for your patience.
Hello @paugier I'm Chiara, following up as editor in chief during those summer months. I just want to let you know that you haven't been forgotten ... hope to find an editor for Fluidimage soon 🤞.
Hello @paugier we are very sorry for making you wait so long! If you are still interested in our review process (I hope so! :innocent:), I'm starting looking for reviewers for your submission.
Thanks a lot for your patience! :pray:
Hello @paugier , I am glad to announce that we have two reviewers for Fluidimage. :tada:
@leahmendelson and @stefanv kindly accepted to take care of this submission: thank you so much to you both! :pray:
Leah, Stefan, before beginning your review, please fill out our pre-review survey. This helps us improve all aspects of our review and better understand our community. No personal data will be shared from this survey - it will only be used in an aggregated format by our Executive Director to improve our processes and programs.
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Please get in touch with any questions or concerns! This review went already a bit out of schedule, I hope a three weeks deadline is ok for you both. Otherwise please let me know, so we can keep track.
This review is then due on November 10th.
Thank you so much again to you both and to Pierre for his patience!
Happy review to all of you!
@leahmendelson, I almost forgot.... Do you mind confirming the github handle of your student, so I can add them to the review acknowledgment? Thank you!
@emmylia321, @leahmendelson and @stefanv, just to tell you that I've just released a new version of fluidimage (0.5.4) with a small fix of a bug with a new version of Matplotlib. There are also wheels for Python 3.13, but in practice they should not be used before scikit-image 0.25 is really released (only 0.25.0rc1 is available right now).
Hello dear reviewers, just checking if you had time to move forward with review. Please let us know! If you need more time I totally understand, I just need to have an insight on the schedule. @emmylia321, @leahmendelson and @stefanv , thank you for your collaboration!
Hi @paugier! Thanks for your submission. Today, I worked on installing the package from source, and here's an initial set of notes I took while doing so:
The README has a broken link to https://en.wikipedia.org/wiki/Particle_image_velocimetry_(PIV) Same for docs frontpage.
CeCILL license is, of course fine and choice of the developers, but worth noting that it is more restrictive than the BSD license used by most of the scientific Python ecosystem.
Package minimal dependency for scikit-image is very old; consider updating? See, e.g., SPEC0
Like with the license, Mercurial is fully the developers' choice, but may exclude significant part of ecosystem developers (I used to use Mercurial, but have no idea how to anymore :man_shrugging:).
Consider shipping example images in separate repository—they really blow up the repo size. See, e.g. pooch.
Consider adding an INSTALL.md or similar with build-from-source instructions; can simply be a link to: https://fluidimage.readthedocs.io/en/latest/build-from-source.html. Many developers will clone repo and look there for how to proceed.
The installation instructions suggest that pdm install --no-self would create a new virtual env, but instead:
$ pdm install --no-self

INFO: Inside an active virtualenv /home/stefan/envs/py312, reusing it.
Set env var PDM_IGNORE_ACTIVE_VENV to ignore it.
When compiling, lots of Pythran warnings, may be worth reporting to Serge:
src/fluidimage/calcul/interpolate/__pythran__/thin_plate_spline.cpp:288:13: warning: possibly dangling reference to a temporary [-Wdangling-reference]
skimage now has thin plate splines, btw: https://scikit-image.org/docs/stable/auto_examples/transform/plot_tps_deformation.html
Not sure if that implementation is useful or good enough for this application, but we'd love feedback :)
make tests resulted in a traceback with:
ModuleNotFoundError: No module named 'coverage.results'
- Upgrading from coverage 7.6.4 to 7.6.7 worked.
- Next, psutil was not found. Huh, something wrong with my psutil install? Reinstalling it fixed the problem.
- Next
ERROR src/fluidimage - AttributeError: module 'cv2' has no attribute 'imread'. - Reinstalling
opencv-pythondid the trick. OK, at this point I'm thinkingpdmmay have done something to mess up my environment. - Also reinstalled
pillow,scipy,kiwisolver,pyyamlto fix import errors.
Yay, test suite passed! Some warnings to resolve:
src/fluidimage/gui/test_monitor.py: 4 warnings
src/fluidimage/test_run_from_xml.py: 4 warnings
src/fluidimage/topologies/test_bos.py: 2 warnings
src/fluidimage/topologies/test_example.py: 11 warnings
src/fluidimage/topologies/test_image2image.py: 10 warnings
src/fluidimage/topologies/test_mean.py: 6 warnings
src/fluidimage/topologies/test_optical_flow.py: 8 warnings
src/fluidimage/topologies/test_piv.py: 12 warnings
src/fluidimage/topologies/test_preproc.py: 8 warnings
/usr/lib64/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=891926) is multi-threaded, use of fork() may lead to deadlocks in the child.
self.pid = os.fork()
Will pick up from here soon!
@stefanv thanks for looking at this. I'm going to answer in more details and fix things, but it is clear that PDM did not do what it should do in particular because you run it from a virtual env used for something else.
I guess things are going to work much better if you don't do that. PDM should create a dedicated environment in /.../fluidimage/.venv
Thanks @stefanv for your notes. I worked on a merge request to improve the situation (https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/116) and opened two issues related to two of your remarks.
The README has a broken link to https://en.wikipedia.org/wiki/Particle_image_velocimetry_(PIV) Same for docs frontpage.
Fixed in https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/116/diffs?commit_id=eaa510beea8938743010f6ef2add5fd2a9e230be
CeCILL license is, of course fine and choice of the developers, but worth noting that it is more restrictive than the BSD license used by most of the scientific Python ecosystem.
CeCILL is equivalent (or better in terms of European laws) than GPL. I wonder how it would be possible than users of a software like fluidimage could be restricted in practice by GPL. However, I asked to the developers if they agree to change to BSD.
Package minimal dependency for scikit-image is very old; consider updating? See, e.g., SPEC0
I updated few minimal dependencies in https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/116/diffs?commit_id=17347a3dca48900011283f2a868b177490d83e52
Like with the license, Mercurial is fully the developers' choice, but may exclude significant part of ecosystem developers (I used to use Mercurial, but have no idea how to anymore 🤷♂️).
I have to admit that I doubt that Mercurial could be a barrier for anyone really wanting to contribute to Fluidimage.
- for beginners, Mercurial is still simpler than Git
- for people used to Git, we have documentation (accessible in particular from our file CONTRIBUTING.md) and our workflow is really simple.
I tend to think that people knowing Git will be able after 2 minutes of reading to run
hg clone ...
cd fluidimage
hg topic my-great-topic-name
hg status
hg commit -m "..."
hg push
More generally, I really think that too much uniformity in tech is bad. For version control, the Git quasi monopoly for open-source is bad. For some aspects, Git is nice, but for some others, it is really bad and old. For example, it is really unfortunate that people cannot safely share history edition and need to push with --force or --force-with-lease. Also the need to use a lot git commit -a is really unfortunate.
Therefore, I consider that it is part of my research tasks to work on one of the alternatives for version control. Mercurial, still used internally at Meta (actually a fork), Google (only the client) and Mozilla, is interesting.
Consider shipping example images in separate repository—they really blow up the repo size. See, e.g.
pooch.
This is indeed interesting. A newly cloned repo (cloned in ~ 5 s so it is still fine) has a size of a bit less than 100MB, which is too much. I opened an issue on this https://foss.heptapod.net/fluiddyn/fluidimage/-/issues/42
Consider adding an INSTALL.md or similar with build-from-source instructions; can simply be a link to: https://fluidimage.readthedocs.io/en/latest/build-from-source.html. Many developers will clone repo and look there for how to proceed.
Done in https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/116/diffs?commit_id=677bd1af0f23fa800eac9466a803a629cdf7cb38
The installation instructions suggest that
pdm install --no-selfwould create a new virtual env, but instead:$ pdm install --no-self  INFO: Inside an active virtualenv /home/stefan/envs/py312, reusing it. Set env var PDM_IGNORE_ACTIVE_VENV to ignore it.
This is really unfortunate that you experienced such problems! Especially because we use good modern tools and everything works well for us with PDM (and also Pixi).
I updated our documentation to avoid your install issue in https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/116/diffs?commit_id=08b63f2c392d4c5a1e2999f527b2531929cbc568
When compiling, lots of Pythran warnings, may be worth reporting to Serge:
With a virtual env correctly setup with PDM, we also have few warnings related to Pythran, but not the same as you! Anyway, I'm going to report this in https://github.com/serge-sans-paille/pythran/
skimagenow has thin plate splines, btw: https://scikit-image.org/docs/stable/auto_examples/transform/plot_tps_deformation.html Not sure if that implementation is useful or good enough for this application, but we'd love feedback :)
I'm going to look at that.
make testsresulted in a traceback with:
Yay, test suite passed! Some warnings to resolve:
All these issues are related to your broken environment. With a correct environment created with PDM, Fluidimage tests pass without warning.
All these issues are related to your broken environment. With a correct environment created with PDM, Fluidimage tests pass without warning.
Great, thanks @paugier! I will rebuild a dedicated virtual environment and re-test. The new documentation says:
You should not run the following commands from a virtual environment not related to Fluidimage.
I think a lot of people start from an existing environment, and after decades of using virtual envs of never tried to get out of one! There is no deactivate command, so not sure how to do that. Looks like pdm --venv .venv or similar may do the trick, though.
Re: the hg and license comments, those were merely observations / data points; totally fine for the project to make opinionated choices, of course. I understand the motivation for libre licenses; one practical issue in our ecosystem is that code cannot flow from GPL packages into BSD libraries. E.g., say you had a good thin-plate splines implementation that we wanted to adopt into scikit-image. But, I'm not pushing you to change the license.
I want to make very clear that my goal with this review is to help the project as much as I can, and to provide some ecosystem context where useful. None of the comments are meant as criticism!
Hello @leahmendelson @emmylia321 @stefanv , I wonder if we can have the reviews in before Christmas? Please let me know if you need any help / info.
Thank you so much for volunteering your time for pyOpenSci.
Hello everybody and happy new year to all of you! I hope you enjoyed some holiday break, we are now back to business and I wondering if we can set a timeline for the reviews. @leahmendelson @emmylia321 @stefanv do you mind letting me know if you are able to finalize your review? Otherwise I can also look for someone else... everyone is busy and this is a volunteer job, so I totally understand if you have issues in moving forward. Please just let us know so we can take the necessary actions.
Thank you so much for your work!
Hello! Sorry, for the late response. I believe I can finish the review before January 19th. If that works well for you, I will send it in then.
Best, Emmelia Hoorn
On Sat, Jan 11, 2025 at 5:48 AM Chiara Marmo @.***> wrote:
Hello everybody and happy new year to all of you! I hope you enjoyed some holiday break, we are now back to business and I wondering if we can set a timeline for the reviews. @leahmendelson https://github.com/leahmendelson @emmylia321 https://github.com/emmylia321 @stefanv https://github.com/stefanv do you mind letting me know if you are able to finalize your review? Otherwise I can also look for someone else... everyone is busy and this is a volunteer job, so I totally understand if you have issues in moving forward. Please just let us know so we can take the necessary actions.
Thank you so much for your work!
— Reply to this email directly, view it on GitHub https://github.com/pyOpenSci/software-submission/issues/194#issuecomment-2585275159, or unsubscribe https://github.com/notifications/unsubscribe-auth/BICG5LTTW64M5XPUPPT6KQL2KEOMVAVCNFSM6AAAAABIQ34K2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOBVGI3TKMJVHE . You are receiving this because you were mentioned.Message ID: @.***>
Sorry for the delays - we should be able to close this out within this and next week.
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Estimated hours spent reviewing: 8
Review Comments
For context, I tested a pre-built install on Windows 11 and a built from source install on ubuntu. I'm holding off on checking off a few items due to the cumulative list of bugs and issues described below.
- [ ] Missing repostatus.org badge
- [ ] README includes a general link to the docs but does not mention installation specifically. It would also likely be worth calling out Mercurial here since it's less common and takes some additional setup.
- [ ] README is missing citation information
- [ ] It would be helpful to provide operating system specific directions where needed (e.g. for venv commands)
- [ ] Broken link on the Build from Source docs page to "fully setup Mercurial with these extensions and learn a bit of Mercurial"
- [ ] A few missing dependencies could be called out in advance (nothing particularly surprising, but always better to be complete): xsimd, opencv-python, pkg-config, pytest
- [ ] Tutorials and examples using
get_path_image_samples()all failed when using the pre-compiled install. Maybe something in the precomplied paths didn't generalize? There was limited documentation for me to debug anything that calls this function. This function worked fine in a built from source version on ubuntu, so possibly something with paths and operating systems? - [ ] Test scripts are all over the place in the repo and don't all run successfully locally. test_image2image.py failed to run locally for me. Looked to be just a typo in the version on the repo. Beyond the test functions in src and the one in examples I couldn't follow the complete set of tests for the package and the tests that exist don't look comprehensive. Is there something buried I'm missing?
- [ ] Example scripts don't all run successfully locally. surface_tracking.py threw attribute errors in particular.
@emmylia321 also had the following notes (running on macOS)
- [ ] Tutorial could be slightly more explicit in parts, though it is generally understandable: E.g. midpage it said, “Let’s go!”, I was not sure if this was a celebration or an instruction to run the file.
- [ ] Got the following error, even though this variable was correctly set to 1 using the instructed code: “SystemError: For performance reason,the environment variable OMP_NUM_THREADS has to be set to "1" before executing a Fluidimage topology.” Fixed this by setting the variable directly in the terminal using:
export OMP_NUM_THREADS=1(I also ran into this when I worked through the PIV computation example). - [ ] Couldn't display the final field displays, fixed this with
result.display(show_correl=False, hist=True. in the script, which makes sense, but it could've been clearer in the tutorial
Hello! Just checking in ... @stefanv , @leahmendelson , @emmylia321 , I hope you are doing well.
Let us know if you have some ideas about a timeline for your review.
Thank you so much for your time!
@cmarmo @paugier Apologies again for the delays. I've updated my previous partial review comment above and am going to call this round of review (from myself and @emmylia321) complete enough. Looking forward to seeing the revisions.
Thank you @leahmendelson and @emmylia321 for all your work! @paugier, feel free to start working on the improvements and your answer to this first round of reviews.
I hope the second one will come soon.
Hello everybody, hope you are all doing well. @stefanv do you think you might be able to finalize this review, or should I look for someone else? @paugier , in the meanwhile feel free to start addressing Leah and Emily's comments, so we can move forward this review. Thanks a lot to you all for your work so far!
@paugier , unfortunately @stefanv could not finalize his review because of too much previous engagements. @Kai-Striega is kindly willing to take over. Thank you so much Kai! We may have a second review by the end of the month.
Hi folks.
I've spent a few hours looking at the project and it looks interesting!
I don't have enough for a full review yet (I'll get there) but I wanted to mention that I'm having significant problems installing fluidimage using pdm (I've never used pdm before so this may be a user error).
I'm trying to follow this section/ When I run the command pdm sync --no-self --clean inside a clean virtual environment, I get a long list of errors from trying to install compiled packages without Cython/Pybind11/pythran. I've also tried ignoring the clean virtual env by setting the PDM_IGNORE_ACTIVE_VENV environment variable. Here is the full log of the command PDM_IGNORE_ACTIVE_VENV=1 pdm sync --no-self --clean, the errors are the same with or without PDM_IGNORE_ACTIVE_VENV set.
Details
$ PDM_IGNORE_ACTIVE_VENV=1 pdm sync --no-self --clean
WARNING: Project requires a python version of >=3.9, The virtualenv is being created for you as it cannot be matched to the right version.
INFO: python.use_venv is on, creating a virtualenv for this project...
Virtualenv is created successfully at /home/kai/Projects/fluidimage/.venv
Synchronizing working set with resolved packages: 194 to add, 0 to update, 0 to remove
✔ Install pip 24.1.2 successful
✔ Install setuptools 71.1.0 successful
✔ Install aiosignal 1.3.1 successful
✔ Install cloudpickle 3.0.0 successful
✔ Install autopep8 2.3.1 successful
✔ Install defusedxml 0.7.1 successful
✔ Install dill 0.3.8 successful
✔ Install distro 1.9.0 successful
✔ Install attrs 23.2.0 successful
✔ Install async-lru 2.0.4 successful
✔ Install certifi 2024.7.4 successful
✔ Install debugpy 1.8.2 successful
✔ Install fonttools 4.53.1 successful
✔ Install docutils 0.21.2 successful
✔ Install arrow 1.3.0 successful
✔ Install aiohttp 3.9.5 successful
✔ Install decorator 5.1.1 successful
✔ Install frozenlist 1.4.1 successful
✔ Install executing 2.0.1 successful
✔ Install beniget 0.4.2.post1 successful
✔ Install asttokens 2.4.1 successful
✔ Install cycler 0.12.1 successful
✔ Install comm 0.2.2 successful
✔ Install alabaster 0.7.16 successful
✔ Install anyio 4.4.0 successful
✔ Install click 8.1.7 successful
✔ Install bleach 6.1.0 successful
✔ Install argon2-cffi-bindings 21.2.0 successful
✔ Install beautifulsoup4 4.12.3 successful
✔ Install accessible-pygments 0.0.5 successful
✔ Install astroid 3.2.4 successful
✔ Install argon2-cffi 23.1.0 successful
✔ Install dask 2024.7.1 successful
✔ Install black 24.4.2 successful
✔ Install charset-normalizer 3.3.2 successful
✖ Install h5py 3.11.0 failed
✔ Install coverage 7.6.0 successful
✔ Install babel 2.15.0 successful
✖ Install contourpy 1.2.1 failed
✖ Install cffi 1.16.0 failed
✔ Install httpcore 1.0.5 successful
✔ Install fqdn 1.5.1 successful
✔ Install jsonschema-specifications 2023.12.1 successful
✔ Install fluiddyn 0.6.4 successful
✔ Install h5netcdf 1.3.0 successful
✔ Install importlib-metadata 8.2.0 successful
✔ Install httpx 0.27.0 successful
✔ Install idna 3.7 successful
✔ Install fsspec 2024.6.1 successful
✔ Install jsonschema 4.23.0 successful
✔ Install gast 0.5.5 successful
✔ Install imagesize 1.4.1 successful
✔ Install jupyter-cache 1.0.0 successful
✔ Install gprof2dot 2024.6.6 successful
✔ Install fastjsonschema 2.20.0 successful
✔ Install jupyter-client 8.6.2 successful
✔ Install imageio 2.34.2 successful
✔ Install h11 0.14.0 successful
✔ Install jupyter-core 5.7.2 successful
✔ Install jinja2 3.1.4 successful
✔ Install markdown-it-py 3.0.0 successful
✔ Install iniconfig 2.0.0 successful
✔ Install jupyterlab 4.2.4 successful
✔ Install jupyter-events 0.10.0 successful
✔ Install jupyterlab-server 2.27.3 successful
✔ Install jupyter-server 2.14.2 successful
✔ Install jupyter-lsp 2.2.5 successful
✔ Install jupytext 1.16.3 successful
✔ Install ipykernel 6.29.5 successful
✔ Install ipython 8.18.1 successful
Installing ipdb 0.13.13... Downloading... 100%
✔ Install ipdb 0.13.13 successful
✔ Install isoduration 20.11.0 successful
✔ Install isort 5.13.2 successful
✔ Install jedi 0.19.1 successful
✔ Install json5 0.9.25 successful
✔ Install jsonpointer 3.0.0 successful
✔ Install mdurl 0.1.2 successful
✔ Install mdit-py-plugins 0.4.1 successful
✔ Install markupsafe 2.1.5 successful
✔ Install jupyterlab-myst 2.4.2 successful
✔ Install networkx 3.2.1 successful
✔ Install jupyterlab-pygments 0.3.0 successful
✔ Install overrides 7.7.0 successful
✔ Install jupyter-server-terminals 0.5.3 successful
✔ Install lazy-loader 0.4 successful
✔ Install meson 1.5.0 successful
✔ Install matplotlib-inline 0.1.7 successful
✔ Install mccabe 0.7.0 successful
✖ Install matplotlib 3.9.1 failed
✖ Install numpy 2.0.1 failed
✔ Install mistune 3.0.2 successful
✔ Install msgpack 1.0.8 successful
✖ Install kiwisolver 1.4.5 failed
✖ Install pandas 2.2.2 failed
✔ Install locket 1.0.0 successful
✔ Install linkify-it-py 2.0.3 successful
✔ Install prometheus-client 0.20.0 successful
✔ Install ply 3.11 successful
✔ Install pure-eval 0.2.3 successful
✔ Install myst-nb 1.1.1 successful
✔ Install mypy-extensions 1.0.0 successful
✔ Install pycparser 2.22 successful
✔ Install meson-python 0.16.0 successful
✖ Install pyfftw 0.14.0 failed
✔ Install ptyprocess 0.7.0 successful
✔ Install multidict 6.0.5 successful
✔ Install nbclient 0.10.0 successful
✔ Install nbconvert 7.16.4 successful
✔ Install nbformat 5.10.4 successful
✔ Install nest-asyncio 1.6.0 successful
✔ Install myst-parser 3.0.1 successful
✔ Install pyparsing 3.1.2 successful
✔ Install ninja 1.11.1.1 successful
✔ Install notebook-shim 0.2.4 successful
✔ Install pygments 2.18.0 successful
✔ Install numpydoc 1.7.0 successful
✔ Install opencv-python 4.10.0.84 successful
✔ Install outcome 1.3.0.post0 successful
✖ Install pyzmq 26.0.3 failed
✔ Install packaging 24.1 successful
✔ Install pillow 10.4.0 successful
✔ Install pandocfilters 1.5.1 successful
✔ Install parso 0.8.4 successful
✔ Install referencing 0.35.1 successful
✔ Install pytest-asyncio 0.23.8 successful
✔ Install partd 1.4.2 successful
✖ Install scipy 1.13.1 failed
✔ Install pathspec 0.12.1 successful
✔ Install pytest 8.3.1 successful
✔ Install pexpect 4.9.0 successful
✔ Install pims 0.7 successful
✔ Install platformdirs 4.2.2 successful
✔ Install pylint 3.2.6 successful
✔ Install pluggy 1.5.0 successful
✔ Install psutil 6.0.0 successful
✔ Install pycodestyle 2.12.0 successful
✔ Install sortedcontainers 2.4.0 successful
✔ Install prompt-toolkit 3.0.47 successful
✔ Install rpds-py 0.19.1 successful
✔ Install pytest-cov 5.0.0 successful
✔ Install python-dateutil 2.9.0.post0 successful
✔ Install six 1.16.0 successful
✔ Install pyproject-metadata 0.8.0 successful
✔ Install pytz 2024.1 successful
✔ Install pydata-sphinx-theme 0.15.4 successful
✔ Install sphinxcontrib-htmlhelp 2.0.6 successful
✔ Install tabulate 0.9.0 successful
✔ Install python-json-logger 2.0.7 successful
✔ Install pyinstrument 4.6.2 successful
✔ Install textual 0.73.0 successful
✔ Install sphinx-copybutton 0.5.2 successful
✔ Install tomlkit 0.13.0 successful
✔ Install rich 13.7.1 successful
✔ Install pythran 0.16.1 successful
✔ Install pyyaml 6.0.1 successful
✔ Install trio 0.26.0 successful
✔ Install requests 2.32.3 successful
✔ Install sniffio 1.3.1 successful
✔ Install stack-data 0.6.3 successful
✔ Install rfc3339-validator 0.1.4 successful
✔ Install rfc3986-validator 0.1.1 successful
✔ Install sphinxcontrib-applehelp 1.0.8 successful
✔ Install terminado 0.18.1 successful
✖ Install scikit-image 0.24.0 failed
✔ Install send2trash 1.8.3 successful
✔ Install simpleeval 0.9.13 successful
✔ Install sphinxcontrib-serializinghtml 1.1.10 successful
✔ Install slicerator 1.1.0 successful
✔ Install snowballstemmer 2.2.0 successful
✔ Install sqlalchemy 2.0.31 successful
✔ Install soupsieve 2.5 successful
✔ Install wcwidth 0.2.13 successful
✔ Install sphinx 7.4.7 successful
✔ Install websocket-client 1.8.0 successful
✔ Install toolz 0.12.1 successful
✔ Install traitlets 5.14.3 successful
✔ Install sphinxcontrib-devhelp 1.0.6 successful
✔ Install transonic 0.7.0 successful
✔ Install sphinxcontrib-jsmath 1.0.1 successful
✔ Install textual-dev 1.5.1 successful
✔ Install zipp 3.19.2 successful
✔ Install tifffile 2024.7.24 successful
✔ Install tinycss2 1.3.0 successful
✔ Install typing-extensions 4.12.2 successful
✔ Install sphinxcontrib-qthelp 1.0.8 successful
✔ Install uc-micro-py 1.0.3 successful
✔ Install tornado 6.4.1 successful
✔ Install uri-template 1.3.0 successful
✔ Install webencodings 0.5.1 successful
✔ Install webcolors 24.6.0 successful
✔ Install urllib3 2.2.2 successful
✔ Install types-python-dateutil 2.9.0.20240316 successful
✔ Install tzdata 2024.1 successful
✔ Install yarl 1.9.4 successful
✖ Install pyzmq 26.0.3 failed
✖ Install kiwisolver 1.4.5 failed
✖ Install h5py 3.11.0 failed
✖ Install pyfftw 0.14.0 failed
✖ Install cffi 1.16.0 failed
✖ Install matplotlib 3.9.1 failed
✖ Install scipy 1.13.1 failed
✖ Install pandas 2.2.2 failed
✖ Install scikit-image 0.24.0 failed
✖ Install numpy 2.0.1 failed
✖ Install contourpy 1.2.1 failed
ERRORS:
add pyzmq failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 402, in _call_hook
raise BackendUnavailable(
...<4 lines>...
)
pyproject_hooks._impl.BackendUnavailable: Cannot import 'scikit_build_core.build'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 86, in wrapper
raise BuildError(str(e)) from e
pdm.exceptions.BuildError: Cannot import 'scikit_build_core.build'
add kiwisolver failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
)
^
File "/home/kai/Projects/fluidimage/.venv/lib/python3.13/site-packages/setuptools/build_meta.py", line 397, in _build_with_temp_dir
self.run_setup()
~~~~~~~~~~~~~~^^
File "/home/kai/Projects/fluidimage/.venv/lib/python3.13/site-packages/setuptools/build_meta.py", line 313, in run_setup
exec(code, locals())
~~~~^^^^^^^^^^^^^^^^
File "<string>", line 15, in <module>
RuntimeError: Missing setup required dependencies: cppy. Installing through pip as recommended ensure one never hits this issue.
add h5py failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Module 'Cython' is missing, please make sure it is specified in the 'build-system.requires' section. If it is
not possible, add it to the project and use '--no-isolation' option.
Showing the last 10 lines of the build output:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/kai/Projects/fluidimage/.venv/lib/python3.13/site-packages/setuptools/dist.py", line 956, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/kai/Projects/fluidimage/.venv/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 989, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/tmp/pdm-build-6tkklu1y/setup_build.py", line 128, in run
from Cython import __version__ as cython_version
ModuleNotFoundError: No module named 'Cython'
add pyfftw failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Module 'numpy' is missing, please make sure it is specified in the 'build-system.requires' section. If it is not
possible, add it to the project and use '--no-isolation' option.
Showing the last 10 lines of the build output:
~~~~~~~~~~~~~~^^^^^^
File "/home/kai/Projects/fluidimage/.venv/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
~~~~~~~~~~~~~~~~~~~~~^^
File "<string>", line 640, in build_extensions
File "<string>", line 588, in make_sniffer
File "<string>", line 572, in __init__
File "<string>", line 171, in __init__
File "<string>", line 90, in get_include_dirs
ModuleNotFoundError: No module named 'numpy'
add cffi failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
running build
running build_py
running build_ext
building '_cffi_backend' extension
cc -pthread -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -fPIC -fPIC -DFFI_BUILDING=1 -DUSE__THREAD -DHAVE_SYNC_SYNCHRONIZE
-I/usr/include/ffi -I/usr/include/libffi -I/home/kai/Projects/fluidimage/.venv/include
-I/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/include/python3.13 -c src/c/_cffi_backend.c -o
build/temp.linux-x86_64-cpython-313/src/c/_cffi_backend.o
src/c/_cffi_backend.c:15:10: fatal error: ffi.h: No such file or directory
15 | #include <ffi.h>
| ^~~~~~~
compilation terminated.
error: command '/usr/bin/cc' failed with exit code 1
add matplotlib failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
The Meson build system
Version: 1.5.0
Source dir: /tmp/pdm-build-31lnetgt
Build dir: /tmp/pdm-build-31lnetgt/.mesonpy-16mw_iqw
Build type: native build
Program python3 found: YES (/home/kai/Projects/fluidimage/.venv/bin/python3)
../meson.build:4:11: ERROR: Command `/home/kai/Projects/fluidimage/.venv/bin/python3 -m setuptools_scm` failed with status 1.
A full log can be found at /tmp/pdm-build-31lnetgt/.mesonpy-16mw_iqw/meson-logs/meson-log.txt
add scipy failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
C linker for the host machine: cc ld.bfd 2.42
C++ compiler for the host machine: c++ (gcc 13.3.0 "c++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0")
C++ linker for the host machine: c++ ld.bfd 2.42
../meson.build:1:0: ERROR: Unknown compiler(s): [['cython'], ['cython3']]
The following exception(s) were encountered:
Running `cython -V` gave "[Errno 2] No such file or directory: 'cython'"
Running `cython3 -V` gave "[Errno 2] No such file or directory: 'cython3'"
A full log can be found at /tmp/pdm-build-4urbyc8e/.mesonpy-zik1ecsu/meson-logs/meson-log.txt
add pandas failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
+ meson setup /tmp/pdm-build-gkkjcf6w /tmp/pdm-build-gkkjcf6w/.mesonpy-nuc2w_2e -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --vsenv
--native-file=/tmp/pdm-build-gkkjcf6w/.mesonpy-nuc2w_2e/meson-python-native-file.ini
The Meson build system
Version: 1.5.0
Source dir: /tmp/pdm-build-gkkjcf6w
Build dir: /tmp/pdm-build-gkkjcf6w/.mesonpy-nuc2w_2e
Build type: native build
../meson.build:5:13: ERROR: Command `/home/kai/Projects/fluidimage/.venv/bin/python /tmp/pdm-build-gkkjcf6w/generate_version.py --print` failed with status 1.
A full log can be found at /tmp/pdm-build-gkkjcf6w/.mesonpy-nuc2w_2e/meson-logs/meson-log.txt
add scikit-image failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C supports arguments -Wno-unused-function: YES
Library m found: YES
Checking if "-Wl,--version-script" : links: YES
Program cython found: NO
../meson.build:59:9: ERROR: Program 'cython' not found or not executable
A full log can be found at /tmp/pdm-build-worsyebe/.mesonpy-btmpe_pn/meson-logs/meson-log.txt
add numpy failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
C linker for the host machine: cc ld.bfd 2.42
C++ compiler for the host machine: c++ (gcc 13.3.0 "c++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0")
C++ linker for the host machine: c++ ld.bfd 2.42
../meson.build:1:0: ERROR: Unknown compiler(s): [['cython'], ['cython3']]
The following exception(s) were encountered:
Running `cython -V` gave "[Errno 2] No such file or directory: 'cython'"
Running `cython3 -V` gave "[Errno 2] No such file or directory: 'cython3'"
A full log can be found at /tmp/pdm-build-d5qunklm/.mesonpy-sf25hauo/meson-logs/meson-log.txt
add contourpy failed:
Traceback (most recent call last):
File "/home/kai/.local/share/uv/python/cpython-3.13.2-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/synchronizers.py", line 29, in install_candidate
self.manager.install(can)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/installers/manager.py", line 33, in install
prepared.build(),
~~~~~~~~~~~~~~^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/models/candidates.py", line 417, in build
self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 84, in wrapper
return func(*args, **kwargs)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/wheel.py", line 26, in build
filename = self._hook.build_wheel(out_dir, self.config_settings, metadata_directory)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 256, in build_wheel
return self._call_hook(
~~~~~~~~~~~~~~~^
"build_wheel",
^^^^^^^^^^^^^^
...<4 lines>...
},
^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
self._subprocess_runner(
~~~~~~~~~~~~~~~~~~~~~~~^
,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cwd=self.source_dir,
^^^^^^^^^^^^^^^^^^^^
extra_environ=extra_environ,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
return log_subprocessor(cmd, cwd, extra_environ=env)
File "/home/kai/.local/share/uv/tools/pdm/lib/python3.13/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
Host machine cpu: x86_64
Program python found: YES (/home/kai/Projects/fluidimage/.venv/bin/python)
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
pybind11-config found: NO
Found CMake: /usr/bin/cmake (3.28.3)
Run-time dependency pybind11 found: NO (tried pkgconfig, config-tool and cmake)
../meson.build:23:15: ERROR: Dependency "pybind11" not found, tried pkgconfig, config-tool and cmake
A full log can be found at /tmp/pdm-build-rxzar10f/.mesonpy-57djard7/meson-logs/meson-log.txt
0:04:56 ✖ Some package operations failed. 11/11
See /home/kai/.local/state/pdm/log/pdm-install-79cbyo58.log for detailed debug log.
[InstallationError]: Some package operations failed.
WARNING: Add '-v' to see the detailed traceback
I've tried installing the packages inside the virtual environment (I don't want them installed globally), however then pdm removes them during the sync. Does this mean that I have to install them globally for pdm to find them?
Thanks @Kai-Striega for looking at this!
PDM will never install things globally. No need to use PDM_IGNORE_ACTIVE_VENV. Just deactivate all virtual environment and use it. PDM is going to create a local venv for you. (Note that it is also UV's behavior.)
I don't know why PDM tries to build so many things. Numpy in particular. It might be because the lock file was a bit old and you use Python 3.13. I relocked to update the lock file so it might work better now.
You can try again with
hg pull
hg up default
rm -rf .venv
# deactivate all venvs
pdm sync --clean -v
I also update the documentation on building from source with PDM.
Thanks @paugier. I've been able to build fluidimage and get the tests to pass. The problem with this is that I'm now testing fluidimage 0.5.4, not 0.5.3 - the version submitted for review. I'm not sure if that's going to be an issue (the code itself looks mostly the same).
With regards to a timeline for the review. I've got a few notes, but I'll need some time to actually collect them into a review. I'll try to get the draft done next weekend, and submit a full review the weekend after that. However, given how large the project is, it may take me an extra weekend.
@paugier I've spent the last few hours going through this. I'll have the formal review by tomorrow. Before that, I've got a couple of questions for @cmarmo:
- Are we assuming to test with free threaded Python?
- I'm currently reviewing fluidimage 0.5.4, not the version that was submitted (0.5.3). Will this be a problem? AFAIK the differences are minimal - it's only that some changes have been made for me to build it more easily
Thank you @Kai-Striega for all your work!
1. Are we assuming to test with free threaded Python?
Unless specific claims in the documentation about the behavior of the package under the free threaded compilation I would say no need for that ... For some reason the documentation is not accessible for me right now, so please forgive the vagueness of my answer...
2. I'm currently reviewing fluidimage 0.5.4, not the version that was submitted (0.5.3). Will this be a problem? AFAIK the differences are minimal - it's only that some changes have been made for me to build it more easily
Nope this is not an issue.
Also, I hope you don't mind I took the liberty to edit your answer pinging the author of the package.
@Kai-Striega I've checked the documentation and there are no specific claims about compiling against free threaded cpython.
Package Review
Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
- [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).
Documentation
The package includes all the following forms of documentation:
- [x] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
- [x] Installation instructions: for the development version of the package and any non-standard dependencies in README.
- [ ] Vignette(s) demonstrating major functionality that runs successfully locally.
- [ ] Function Documentation: for all user-facing functions.
- [ ] Examples for all user-facing functions.
- [x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
- [x] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a
pyproject.tomlfile or elsewhere.
Readme file requirements The package meets the readme requirements below:
- [x] Package has a README.md file in the root directory.
The README should include, from top to bottom:
- [x] The package name
- [ ] Badges for:
- [x] Continuous integration and test coverage,
- [x] Docs building (if you have a documentation website),
- [ ] A repostatus.org badge,
- [x] Python versions supported,
- [x] Current package version (on PyPI / Conda).
NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)
- [x] Short description of package goals.
- [x] Package installation instructions
- [x] Any additional setup required to use the package (authentication tokens, etc.)
- [ ] Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- [ ] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
- [x] Link to your documentation website.
- [x] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
- [ ] Citation information
Usability
Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole. Package structure should follow general community best-practices. In general please consider whether:
- [ ] Package documentation is clear and easy to find and use.
- [x] The need for the package is clear
- [ ] All functions have documentation and associated examples for use
- [x] The package is easy to install
Functionality
- [x] Installation: Installation succeeds as documented.
- [x] Functionality: Any functional claims of the software been confirmed.
- [x] Performance: Any performance claims of the software been confirmed.
- [ ] Automated tests:
- [x] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [ ] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
- [x] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
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A few notable highlights to look at:
- [x] Package supports modern versions of Python and not End of life versions.
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For packages also submitting to JOSS
- [ ] The package has an obvious research application according to JOSS's definition in their submission requirements.
Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.
The package contains a paper.md matching JOSS's requirements with:
- [ ] A short summary describing the high-level functionality of the software
- [ ] Authors: A list of authors with their affiliations
- [ ] A statement of need clearly stating problems the software is designed to solve and its target audience.
- [ ] References: With DOIs for all those that have one (e.g. papers, datasets, software).
Final approval (post-review)
- [ ] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.
Estimated hours spent reviewing: 10
Review Comments
The package author has obviously invested a significant amount of time and effort into this package. And it shows in the scale and complexity of the project. After having some initial issues building the project (due to myself not being experienced with pdm) I managed to get the test suite and benchmarks to run, in addition to playing around with some of the functionality locally. Talking about tests, they are interleaved with the source code, I usually prefer to have a distinct test/ directory, however that is a matter of preference.