M4 Mac OS Install #1175

sebastienjanel · 2025-06-16T08:07:23Z

sebastienjanel
Jun 16, 2025

Hi,

what's the best option to install TopoStats on a M4 Mac?
I reckon Python 3.13 and Numpy 2 are not supported, is it correct?

Thank you

Answered by sebastienjanel

Jun 16, 2025

Ok I got it. Topostats was installed in the system version of Python, even though I was in the venv in PyCharm. I uninstalled it with /Library/Frameworks/Python.framework/Versions/3.13/bin/python3 -m pip uninstall topostats, then activated the venv source .venv/bin/activate, and reinstalled pip install -e .
Probably this was a previous system-wide, ghost installation.

View full answer

SylviaWhittle · 2025-06-16T09:13:10Z

SylviaWhittle
Jun 16, 2025
Maintainer

Hey @sebastienjanel :)

An M4 Mac should work just like my M1 Mac I think, so I wouldn't expect any difference.

You are correct about the Python and numpy support. We are trying to get TopoStats working with 3.12 & 3.13 but are experiencing issues with dependencies. Python 3.11 is stable for TopoStats. Similarly for numpy 2.X, we are finding issues with dependencies using deprecated numpy functionality, so we are actively addressing this but don't consider it stable yet.

The documentation for installation should work for you (I use an M1 Mac and it is fine for me), but here is a brief TL;DR:

I'd recommend creating a Python 3.11 virtual environment using venv anaconda or pyenv and then do one of the two following options:

For the latest stable TopoStats release, run pip install topostats in your virtual environment
Or, if you know how to clone GitHub repositories, you can get the latest development version by cloning this repo to your computer, navigating to the cloned directory while in your virtual environment and running pip install -e .

4 replies

sebastienjanel Jun 16, 2025
Author

I cloned the Github link in PyCharm using Python 3.10 interpreter and Numpy 1.26. I ran pip install -e . and got version 2.2.1. Isn't it 2.3.0 the last version?

SylviaWhittle Jun 16, 2025
Maintainer

I cloned the Github link in PyCharm using Python 3.10 interpreter and Numpy 1.26. I ran pip install -e . and got version 2.2.1. Isn't it 2.3.0 the last version?

Ah. Yeah we are a quite confused about this, about a week or so ago, pip started installing numpy 2.X when running pip install -e . and we don't know why, since it isn't supported by one of our dependencies... It was working before fine. It's an ongoing issue but don't yet have a good answer sadly.

I think the main issue you're experiencing loading the files may not be due to the numpy thing though. I just received the files from Alice so I'll have a look now.

SylviaWhittle Jun 16, 2025
Maintainer

Got it working.

Here is what I did:

Using the latest development build of TopoStats (GitHub repo clone) and pip install -e .:

Numpy info in case relevant later:

Download your images.
Change the extension of the .spm file you sent to .jpk
Use gwyddion to open the file
In gwyddion, "save as" and save the file as a .gwy file
Get topostats to process the image
- Create a directory
- Create a sub-directory called data
- Place the .gwy image in there
- Go back to the parent directory
- topostats create-config -f config.yaml
- Edit the config file so the file_ext parameter is .gwy
- Edit the config file so the summary_stats > run option is False (just because this will fill up the output log and make it harder to read)
- Edit the config file so channel is "[3] Contact Point Offset" (After a failed attempt at running topostats, which told me that was the only channel present)
- Run topostats with topostats -c config.yaml process
- It works (on my machine at least)

Maybe give that a go and see if you get what you need? The config will need tweaking of course.

Here is the output btw.

The larger blobs aren't detected because of the config's maximum size I think

sebastienjanel Jun 16, 2025
Author

That works!
(In the first place I did not write the channel name correctly...)

Should I contact Paul Muller to add support for JPK QI Images? I tried replacing the filename with no success.
Is there a way to automate jpk-qi-image to gwy conversion?

ns-rse · 2025-06-16T10:07:44Z

ns-rse
Jun 16, 2025
Maintainer

I cloned the Github link in PyCharm using Python 3.10 interpreter and Numpy 1.26. I ran pip install -e . and got version 2.2.1. Isn't it 2.3.0 the last version?

Sure its not v2.3.1?

I've just created a fresh virtual environment, cloned the repository, checked the tags, installed and checked the version of topostats and numpy that have been installed...

Create a new virtualenv

❱ mktmpenv -p python3.11 
created virtual environment CPython3.11.11.final.0-64 in 200ms
  creator CPython3Posix(dest=/home/neil/.virtualenvs/tmp-9b400ec0d8531bd, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/neil/.local/share/virtualenv)
    added seed packages: pip==25.1.1, setuptools==80.7.1, wheel==0.45.1
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator
virtualenvwrapper.user_scripts creating /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/bin/predeactivate
virtualenvwrapper.user_scripts creating /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/bin/postdeactivate
virtualenvwrapper.user_scripts creating /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/bin/preactivate
virtualenvwrapper.user_scripts creating /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/bin/postactivate
virtualenvwrapper.user_scripts creating /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/bin/get_env_details

Clone the repository

❱ git clone [email protected]:AFM-SPM/TopoStats.git
Cloning into 'TopoStats'...
remote: Enumerating objects: 29188, done.
remote: Counting objects: 100% (1732/1732), done.
remote: Compressing objects: 100% (271/271), done.
remote: Total 29188 (delta 999), reused 1705 (delta 984), pack-reused 27456 (from 2)
Receiving objects: 100% (29188/29188), 1013.79 MiB | 18.14 MiB/s, done.
Resolving deltas: 100% (20478/20478), done.

Go into the cloned repository and list tags

❱ cd TopoStats
❱ git tag --list
v2.3.1      v2.2.1      v2.2.post0  v2.2.0      v2.1.2      v2.1.1      v2.1.0      v2.0.0      v2.3.0

Install and check version

❱ pip install -e .
Obtaining file:///home/neil/tmp/TopoStats
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
Collecting art (from topostats==2.3.2.dev487+g961c60ba)
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Collecting AFMReader@ git+https://github.com/AFM-SPM/AFMReader@main (from topostats==2.3.2.dev487+g961c60ba)
  Cloning https://github.com/AFM-SPM/AFMReader (to revision main) to /tmp/pip-install-yhr3dckm/afmreader_1ee2adb5a7464baa8953a916963e083b
  Running command git clone --filter=blob:none --quiet https://github.com/AFM-SPM/AFMReader /tmp/pip-install-yhr3dckm/afmreader_1ee2adb5a7464baa8953a916963e083b
  Resolved https://github.com/AFM-SPM/AFMReader to commit 794e2d100217be949e3d2fe83d159576273a18c6
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
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Collecting h5py (from topostats==2.3.2.dev487+g961c60ba)
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Collecting numpyencoder@ git+https://github.com/AFM-SPM/numpyencoder@master (from topostats==2.3.2.dev487+g961c60ba)
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  Running command git clone --filter=blob:none --quiet https://github.com/AFM-SPM/numpyencoder /tmp/pip-install-yhr3dckm/numpyencoder_e9e4b8462a2949189f5775a442c5d354
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  Preparing metadata (setup.py) ... done
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Collecting fonttools>=4.22.0 (from matplotlib->topostats==2.3.2.dev487+g961c60ba)
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Building wheels for collected packages: topostats, AFMReader, numpyencoder
  Building editable for topostats (pyproject.toml) ... done
  Created wheel for topostats: filename=topostats-2.3.2.dev487+g961c60ba-0.editable-py3-none-any.whl size=21467 sha256=c5329acafc4b76847054f0e79dd8fa28b87741977189e7fd11aa7959c04eb361
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  Building wheel for AFMReader (pyproject.toml) ... done
  Created wheel for AFMReader: filename=afmreader-0.0.5-py3-none-any.whl size=39855 sha256=a2efab128221f84abdaeee021eb271a6a5ee770ee3955d15a952782710c3f904
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  DEPRECATION: Building 'numpyencoder' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'numpyencoder'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for numpyencoder (setup.py) ... done
  Created wheel for numpyencoder: filename=numpyencoder-0.3.2-py3-none-any.whl size=3086 sha256=f7e6921a72b5d6dff4d0ad0cef698a095073da45b36a57bf2ea83a92101d5fc1
  Stored in directory: /tmp/pip-ephem-wheel-cache-2w6avs_w/wheels/9c/31/f9/b1562a5fcf592993bdf6cb653aca01c4ed3d658d983d2ebd65
Successfully built topostats AFMReader numpyencoder
Installing collected packages: wcwidth, schema, pytz, pure-eval, ptyprocess, namex, libclang, flatbuffers, cheap-repr, argparse, wrapt, urllib3, tzdata, typing-extensions, traitlets, tqdm, toolz, threadpoolctl, termcolor, tensorflow-io-gcs-filesystem, tensorboard-data-server, six, ruamel.yaml.clib, pyyaml, pyparsing, pygments, psygnal, psutil, protobuf, prompt_toolkit, pillow, pexpect, parso, packaging, opt-einsum, numpy, networkx, mdurl, MarkupSafe, markdown, loguru, llvmlite, kiwisolver, joblib, idna, grpcio, gast, fonttools, executing, et-xmlfile, docstring-parser, decorator, cycler, charset_normalizer, certifi, asttokens, art, absl-py, werkzeug, tifffile, stack_data, snoop, scipy, ruamel.yaml, requests, qtpy, python-dateutil, optree, openpyxl, numpyencoder, numba, ml-dtypes, matplotlib-inline, markdown-it-py, lazy-loader, jedi, imageio, igor2, h5py, google-pasta, contourpy, biopython, astunparse, tensorboard, superqt, scikit-learn, scikit-image, rich, pyconify, pandas, matplotlib, ipython, topoly, seaborn, keras, tensorflow, pySPM, magicgui, skan, AFMReader, topostats
Successfully installed AFMReader-0.0.5 MarkupSafe-3.0.2 absl-py-2.3.0 argparse-1.4.0 art-6.5 asttokens-3.0.0 astunparse-1.6.3 biopython-1.85 certifi-2025.6.15 charset_normalizer-3.4.2 cheap-repr-0.5.2 contourpy-1.3.2 cycler-0.12.1 decorator-5.2.1 docstring-parser-0.16 et-xmlfile-2.0.0 executing-2.2.0 flatbuffers-25.2.10 fonttools-4.58.4 gast-0.6.0 google-pasta-0.2.0 grpcio-1.73.0 h5py-3.14.0 idna-3.10 igor2-0.5.12 imageio-2.37.0 ipython-8.37.0 jedi-0.19.2 joblib-1.5.1 keras-3.10.0 kiwisolver-1.4.8 lazy-loader-0.4 libclang-18.1.1 llvmlite-0.44.0 loguru-0.7.3 magicgui-0.10.1 markdown-3.8 markdown-it-py-3.0.0 matplotlib-3.10.3 matplotlib-inline-0.1.7 mdurl-0.1.2 ml-dtypes-0.5.1 namex-0.1.0 networkx-3.5 numba-0.61.2 numpy-2.0.2 numpyencoder-0.3.2 openpyxl-3.1.5 opt-einsum-3.4.0 optree-0.16.0 packaging-25.0 pandas-2.3.0 parso-0.8.4 pexpect-4.9.0 pillow-11.2.1 prompt_toolkit-3.0.51 protobuf-5.29.5 psutil-5.9.8 psygnal-0.13.0 ptyprocess-0.7.0 pure-eval-0.2.3 pySPM-0.6.3 pyconify-0.2.1 pygments-2.19.1 pyparsing-3.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.2 qtpy-2.4.3 requests-2.32.4 rich-14.0.0 ruamel.yaml-0.18.14 ruamel.yaml.clib-0.2.12 schema-0.7.7 scikit-image-0.25.2 scikit-learn-1.7.0 scipy-1.15.3 seaborn-0.13.2 six-1.17.0 skan-0.12.2 snoop-0.6.0 stack_data-0.6.3 superqt-0.7.4 tensorboard-2.19.0 tensorboard-data-server-0.7.2 tensorflow-2.19.0 tensorflow-io-gcs-filesystem-0.37.1 termcolor-3.1.0 threadpoolctl-3.6.0 tifffile-2025.6.11 toolz-1.0.0 topoly-1.1.0 topostats-2.3.2.dev487+g961c60ba tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.14.0 tzdata-2025.2 urllib3-2.4.0 wcwidth-0.2.13 werkzeug-3.1.3 wrapt-1.17.2
 10:47:05 am BST  neil@haldane  ~/tmp/TopoStats  G  main   
(tmp-9b400ec0d8531bd) ❱ pip show topostats
Name: topostats
Version: 2.3.2.dev487+g961c60ba
Summary: Automated Analysis for Atomic Force Microscopy Images of Biomolecules
Home-page: 
Author: 
Author-email: TopoStats Team <[email protected]>, Alice Pyne <[email protected]>, Sylvia Whittle <[email protected]>, Neil Shephard <[email protected]>, Max Gamill <[email protected]>, Jean Du <[email protected]>
License: GNU Lesser GPLv3 only
Location: /home/neil/.virtualenvs/tmp-9b400ec0d8531bd/lib/python3.11/site-packages
Editable project location: /home/neil/tmp/TopoStats
Requires: AFMReader, art, h5py, keras, matplotlib, numpy, numpyencoder, pandas, pyyaml, ruamel.yaml, schema, scikit-image, scipy, seaborn, skan, snoop, tensorflow, topoly, tqdm
Required-by: 
 10:48:33 am BST  neil@haldane  ~/tmp/TopoStats  G  main   
(tmp-9b400ec0d8531bd) ❱ pip show numpy | head -n20
Name: numpy
Version: 2.0.2
Summary: Fundamental package for array computing in Python
Home-page: https://numpy.org
Author: Travis E. Oliphant et al.
Author-email: 
License: Copyright (c) 2005-2024, NumPy Developers.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

    * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.

I get topostats-2.3.2.dev487+g961c60ba along with numpy-2.0.2. Versions for TopoStats are derived automatically using the setuptools_scm which is why we see the last tag as v2.3.1 but the installed version as 2.3.2.dev487+g961c60ba.

Numpy 2.x issue was down to a dependency pySPM not supporting newer versions of Numpy, which I fixed upstream. We then encountered another issue with numpyencoder not working with newer version of Numpy because Numpy deprecated support for some types. I've a pending pull request to solve this but in the mean time we forked numpyencoder and fixed the issue there and we install that for the time being (can't make a release to PyPI until that is resolved upstream as you can't have dependencies install from GitHub when installing from PyPI).

To check things work in this fresh install I then installed the test suite (pip install -e .[tests]) and tried running the test suite (pytest -n 10 to run the tests in parallel) and they passed.

It could be that the wrong environment has been picked up by PyCharm. I don't use PyCharm so have no idea about how it creates and manages virtual environments.

Re : Python 3.13

We hope to support newer versions of Python > 3.11 once one of the packages we depend on supports this (see issue #927 where we are tracking this).

0 replies

sebastienjanel · 2025-06-16T10:31:35Z

sebastienjanel
Jun 16, 2025
Author

It’s 2.2.1, and comes with some Exceptions. Numpy 1.26.4 Python 3.10 ``` % topostats -v Exception ignored in: <_io.FileIO name='/Users/sebastienjanel/Pasteur/Developpements/TopoStats/TopoStats-2025-06-16-12-28-51.log' mode='ab' closefd=True> Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/topostats/statistics.py", line 8, in <module> LOGGER = setup_logger(LOGGER_NAME) ResourceWarning: unclosed file <_io.TextIOWrapper name='/Users/sebastienjanel/Pasteur/Developpements/TopoStats/TopoStats-2025-06-16-12-28-51.log' mode='a' encoding='UTF-8'> Exception ignored in: <_io.FileIO name='/Users/sebastienjanel/Pasteur/Developpements/TopoStats/TopoStats-2025-06-16-12-28-51.log' mode='ab' closefd=True> Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/topostats/processing.py", line 31, in <module> LOGGER = setup_logger(LOGGER_NAME) ResourceWarning: unclosed file <_io.TextIOWrapper name='/Users/sebastienjanel/Pasteur/Developpements/TopoStats/TopoStats-2025-06-16-12-28-51.log' mode='a' encoding='UTF-8'> Installed version of TopoStats: 2.2.1 ``` Actually `topostats -v` and `pip show topostats` actually return different versions, 2.2.1 vs 2.3.2.dev487+g961c60ba! Test install do not work : `pip install -e .[tests] zsh: no matches found: .[tests]`

0 replies

ns-rse · 2025-06-16T10:49:28Z

ns-rse
Jun 16, 2025
Maintainer

There is something strange going on with your virtual environments I think.

You say you are using Python 3.10 but the output shows that when you call topostats -v it is using a version installed under Python 3.13 as shown by this line in your log file...

  File "/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/topostats/statistics.py", line 8, in <module>

...the key bit being Versions/3.13/lib/python3.13/site-packages/. If it were using your 3.10 environment it would read 3.10 and not 3.13.

What does which python show?

Could it be that PyCharm has only activated the virtual environment within itself and not in the shell that is being used?

4 replies

sebastienjanel Jun 16, 2025
Author

Indeed. I'm not familiar with the pip install -e . way. I'll double check the python env.
Is there a way to launch a main script from a python file like for dev ?

sebastienjanel Jun 16, 2025
Author

Ok I got it. Topostats was installed in the system version of Python, even though I was in the venv in PyCharm. I uninstalled it with /Library/Frameworks/Python.framework/Versions/3.13/bin/python3 -m pip uninstall topostats, then activated the venv source .venv/bin/activate, and reinstalled pip install -e .
Probably this was a previous system-wide, ghost installation.

Answer selected by sebastienjanel

ns-rse Jun 17, 2025
Maintainer

Glad to hear you sorted it @sebastienjanel.

pip install -e . means you are installing from the current directory (typically a cloned repository) rather than from the Python Package Index. The -e flag means that the install is editable so that any changes made to the files within the cloned repository are reflected when the code is run.

Is there a way to launch a main script from a python file like for dev ?

You can run Python scripts at the command line with python <some_python_file.py>. Whether that does what you expect depends on how <some_python_file.py> has been written.

For TopoStats we use what is known as an entry point defined under [project.scripts] in the pyproject.toml configuration file. When the package is installed the command topostats is made available which points to the topostats.entry_point:entry_point() function which provides the interface to the argument parsing and invoking the different sub-commands and their arguments.

sebastienjanel Jun 17, 2025
Author

Thank you for the explanation.

M4 Mac OS Install #1175

Uh oh!

sebastienjanel Jun 16, 2025

Replies: 4 comments · 8 replies

Uh oh!

SylviaWhittle Jun 16, 2025 Maintainer

Uh oh!

sebastienjanel Jun 16, 2025 Author

Uh oh!

SylviaWhittle Jun 16, 2025 Maintainer

Uh oh!

SylviaWhittle Jun 16, 2025 Maintainer

Uh oh!

sebastienjanel Jun 16, 2025 Author

Uh oh!

ns-rse Jun 16, 2025 Maintainer

Create a new virtualenv

Clone the repository

Go into the cloned repository and list tags

Install and check version

Re : Python 3.13

Uh oh!

Uh oh!

sebastienjanel Jun 16, 2025 Author

Uh oh!

ns-rse Jun 16, 2025 Maintainer

Uh oh!

sebastienjanel Jun 16, 2025 Author

Uh oh!

Uh oh!

sebastienjanel Jun 16, 2025 Author

Uh oh!

ns-rse Jun 17, 2025 Maintainer

Uh oh!

sebastienjanel Jun 17, 2025 Author

sebastienjanel
Jun 16, 2025

Replies: 4 comments 8 replies

SylviaWhittle
Jun 16, 2025
Maintainer

sebastienjanel Jun 16, 2025
Author

SylviaWhittle Jun 16, 2025
Maintainer

SylviaWhittle Jun 16, 2025
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sebastienjanel Jun 16, 2025
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ns-rse
Jun 16, 2025
Maintainer

sebastienjanel
Jun 16, 2025
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ns-rse
Jun 16, 2025
Maintainer

sebastienjanel Jun 16, 2025
Author

sebastienjanel Jun 16, 2025
Author

ns-rse Jun 17, 2025
Maintainer

sebastienjanel Jun 17, 2025
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