Support dynamic version for dev and releases.

[ccoulombe]

When installing from HEAD, this would allow one to have traceable reproducibility.
A local wheel built today from a fresh clone, would be tagged alphafold3-3.0.2.dev113+gebfe70a27.d20260206-cp313-cp313-linux_x86_64.whl.

The version is incremented from the current tag.
A dev release suffix which show that 113 commits have been made since.
A local version +gebfe70a27.d20260206 which means :

• gebfe70a27 (g+short commit)
• d20260206 (d+date)

Hence it is easy to know which build/commit a user used as it is described in the file name.

Ref:

• https://scikit-build-core.readthedocs.io/en/latest/configuration/dynamic.html
• https://setuptools-scm.readthedocs.io/en/latest/usage/#default-versioning-scheme

[Augustin-Zidek]

Wouldn't the CMake part need to be updated as well?

[ccoulombe]

Which cmake part more precisely are you referring to?

…

On Fri, Mar 6, 2026, 12:29 Augustin Žídek ***@***.***> wrote: *Augustin-Zidek* left a comment (google-deepmind/alphafold3#617) <#617 (comment)> Wouldn't the CMake part need to be updated as well? — Reply to this email directly, view it on GitHub <#617 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFMODOD4Y4J6FLI4IIFI3IL4PMDIHAVCNFSM6AAAAACUFYMWQ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMJTGA2DCMBZGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Augustin-Zidek]

Sorry for the late reply. Will this work correctly with this line in CMakeLists.txt:

project(
  "${SKBUILD_PROJECT_NAME}"
  LANGUAGES CXX
  VERSION "${SKBUILD_PROJECT_VERSION}")

The ${SKBUILD_PROJECT_VERSION} variable in particular.

[ccoulombe]

With the changes from this PR, I was able to build ebfe70a27a6a1ad18c77664191c5f7fa486ebee9 of AF3.

  Created wheel for alphafold3: filename=alphafold3-3.0.2.dev113+gebfe70a27.d20260402-cp313-cp313-linux_x86_64.whl size=242965375 sha256=221d6b8d0464d5018a373e5dd1aab767cb3f0eb75883e0e74024b2f23cdef61c

And adding some print status from CMake:

  -- Detecting CXX compile features - done
  -- >>> SKBUILD_PROJECT_VERSION = 3.0.2
  -- >>> PROJECT_VERSION = 3.0.2

Thus, I'd say yes. Esp. since it is scikit-build-core that manage the version via

metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"

From the documentation,

If you need to set the CMake project version without scikit-build-core (which provides ${SKBUILD_PROJECT_VERSION})

we could infer that it manages the variable SKBUILD_PROJECT_VERSION correctly.

[Augustin-Zidek]

Right, I am still worried about a few things:

1. Will this work if people download a zip of the source code without the .git directory? I.e. what version will I get if I remove the .git directory? Is there a fallback mechanism?
2. Does python3 run_alphafold.py --version work?
3. Does the version still work correctly when run in the Docker container? (Docker might exclude the .git directory when building)
4. Isn't a [build-system] section missing (see e.g. https://pydevtools.com/handbook/how-to/how-to-add-dynamic-versioning-to-uv-projects/)

[ccoulombe]

Let me work on each point...

Regarding

Does python3 run_alphafold.py --version work?

There is currently no argument --version, but one could think of adding one :)

Regarding

4. Isn't a [build-system] section missing (see e.g. https://pydevtools.com/handbook/how-to/how-to-add-dynamic-versioning-to-uv-projects/)

The section is already present in

alphafold3/pyproject.toml

Line 1 in 87bd9e6

[build-system]

and setuptools-scm is already part (pulled) from scikit-build-core : scikit_build_core/metadata/setuptools_scm.py.
And see:
https://github.com/scikit-build/scikit-build-core/blob/fc4ea500205d0ee79b5505305a184970476abfc1/src/scikit_build_core/metadata/setuptools_scm.py#L51-L54

[Augustin-Zidek]

There is currently no argument --version, but one could think of adding one :)

There isn't an explicit one, but I think abseil flags library adds one.

and setuptools-scm is already part (pulled) from scikit-build-core : scikit_build_core/metadata/setuptools_scm.py.

TIL, thanks for investigating!

[ccoulombe]

So, regarding the items from #617 (comment)

---

1. This does not work when no .git folder is found. See scikit-build-core/setuptools-scm

It fails with:

  ValueError: setuptools-scm was unable to detect version for /home/coulombc/alphafold3.

  Make sure you're either building from a fully intact git repository or PyPI tarballs. Most other sources (such as GitHub's tarballs, a git checkout without the .git folder) don't contain the necessary metadata and will not work.

  For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+https://github.com/user/proj.git#egg=proj

Personally, I would bluntly let the installation fails when a user used the .zip directly instead of pip install git+<> and document the correct installation procedure.

Else, a static version could act as a fallback mechanism:

[tool.setuptools_scm]
fallback_version = "3.0.1"

Ref: https://setuptools-scm.readthedocs.io/en/latest/config/#core-configuration

What do you prefer?

Also note, that one can always override the version with an env. variable: SETUPTOOLS_SCM_PRETEND_VERSION.

---

2. There is no version automagically added, but I suppose it could be added if needed

$ python run_alphafold.py --helpfull | rg version
$ python run_alphafold.py --version
FATAL Flags parsing error: Unknown command line flag 'version'
Pass --helpshort or --helpfull to see help on flags.

---

3. Since .git is not excluded from the dockerignore file, it is my understanding that it would be copied hence the dynamic version would work. But I do not have docker to 100% test it out.

Also depends on choice made for 1.

---

4. scikit-build-core does pull dynamically some build.requires like ninja, cmake, or setuptools-scm.
   On second thought, I do prefer when things are explicit so I will add setuptools-scm. But if you prefer, the three can be removed, as the build system warns:

2026-04-10 23:15:00,200 - scikit_build_core - WARNING - ninja should not be in build-system.requires - scikit-build-core will inject it as needed

---

Based on the decision for 1. I would remove the file src/alphafold3/version.py and add the section

[tool.setuptools_scm]  
write_to = "src/alphafold3/version.py"

to the pyproject.toml so that the version.py file is automatically generated.
Else, in case the version.py needs to stay, I would use importlib.metadata.
It would look like:

>>> from alphafold3 import version
>>> version.__version__
'3.0.1.dev224+g35955279b.d20260410'