Remove setup.py information from info.py #551

matthew-brett · 2023-11-09T22:37:13Z

Shift away from info.py as source of setup information.

codecov · 2023-11-09T22:44:57Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (dc97dbf) 84.71% compared to head (adfaf66) 84.69%.
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #551      +/-   ##
==========================================
- Coverage   84.71%   84.69%   -0.02%     
==========================================
  Files         297      297              
  Lines       27632    27592      -40     
  Branches     3361     3361              
==========================================
- Hits        23409    23370      -39     
+ Misses       3269     3268       -1     
  Partials      954      954

Files	Coverage Δ
nipy/__init__.py	`69.23% <100.00%> (-6.96%)`	⬇️
nipy/info.py	`100.00% <100.00%> (ø)`

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pyproject.toml

effigies

Some quick notes. Nothing blocking.

effigies · 2023-11-10T13:47:41Z

pyproject.toml

+build = [
+    'meson-python>=0.13',
+    'wheel',
+    'setuptools>=67',
+    'ninja',
+    'Cython>=3',
+    'numpy>=1.22',
+    'spin==0.3',
+    'build',
+]
+default = [
+    'numpy>=1.22',
+    'scipy>=1.8',
+    'nibabel>=3.2',
+    'sympy>=1.9',
+    'transforms3d'
+]


IMO build and default don't make much sense. nipy[default] is equivalent to nipy and now you have duplication.

I'm not sure what nipy[build] is adding, since to install it you will already need something capable of building, while also duplicating (and extending?) the build-system.requires table.

@stefanv - any thoughts? I copied this brainlessly from scikit-image: https://github.com/scikit-image/scikit-image/blob/main/pyproject.toml#L46

@stefanv - any reason not to just delete the build and default sections of the optional-dependencies?

effigies · 2023-11-10T13:52:02Z

pyproject.toml

 [build-system]
 build-backend = "mesonpy"
 requires = [
  "meson-python>=0.13",
+  "ninja",


I'm able to build without this. Is ninja a dependency of meson-python that you just want to be explicit about? Do you actually depend on ninja-specifics, or could the other build tools stop using it without you needing to change anything?

I was getting errors trying to build without it, for the wheel builds. I'm afraid I don't understand the build mechanics well enough to respond. If ninja is missing, with meson-python use something else?

How are you building? I'm using python -m build.

pip wheel ...

Hmm. Possibly an old pip? I just created a fresh environment:

$ mamba create -n tmp python=3.11 $ mamba activate tmp $ pip wheel . Processing /home/chris/Projects/nipy/nipy Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Building wheels for collected packages: nipy Building wheel for nipy (pyproject.toml) ... done Created wheel for nipy: filename=nipy-0.5.1.dev1-cp311-cp311-linux_x86_64.whl size=1916097 sha256=7ff5b2a9a9fe053c913dd2e487ee8c8fd11991893cf96e0f806846c79d17cd8b Stored in directory: /tmp/pip-ephem-wheel-cache-sn4mrur1/wheels/a1/58/f7/1af5aca9b8327defaf19028fc61c6f4850bd54b33e92f89a43 Successfully built nipy $ pip --version pip 23.3.1 from /home/chris/mambaforge/envs/tmp/lib/python3.11/site-packages/pip (python 3.11)

pyproject.toml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

This reverts commit ee349e8, and adds some comments.

stefanv · 2023-11-10T20:55:14Z

I'm curious why dropping ninja works. You need to get it into your environment somehow, and it is not installed as a dependency of meson or meson-python.

stefanv · 2023-11-10T21:12:58Z

I just verified that, if ninja is not presence, it will fail on a build. It can be confusing to test, because if ninja is already on the PATH (from a different venv), it will still be picked up and used.

To see that in action, clone https://github.com/stefanv/test-ninja-missing-compile-failure and run nox, ensuring that ninja is NOT on the PATH.

effigies · 2023-11-10T21:13:45Z

I don't have ninja installed in my path, and using pipx run build to run in a completely clean environment, I see:

$ pipx run build
[...]
Build targets in project: 16

nipy 0.5.1.dev1

  User defined options
    Native files: /tmp/build-via-sdist-48bra0w8/nipy-0.5.1.dev1/.mesonpy-x0vcp63g/meson-python-native-file.ini
    buildtype   : release
    b_ndebug    : if-release
    b_vscrt     : md

Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/build-env-bge1hi3c/bin/ninja

So it does seem to be getting pulled in somewhere. I don't know how right now...

effigies · 2023-11-10T21:20:15Z

Hmm. Missed an important bit:

$ pipx run build 
* Creating venv isolated environment...
* Installing packages in isolated environment... (cython>=3, meson-python>=0.13, numpy==1.22; python_version >= '3.7' and python_version < '3.9', numpy>=1.25; python_version > '3.8', setuptools)
* Getting build dependencies for sdist...
* Installing packages in isolated environment... (ninja >= 1.8.2)

I would guess meson is injecting it.

Edit: https://github.com/mesonbuild/meson-python/blob/551962d/mesonpy/__init__.py#L993-L1000

effigies · 2023-11-10T21:22:07Z

To see that in action, clone https://github.com/stefanv/test-ninja-missing-compile-failure and run nox, ensuring that ninja is NOT on the PATH.

I can confirm that pipx run nox doesn't work, but pipx run build does.

matthew-brett · 2023-11-10T21:28:55Z

Sounds like it would be safer to add it back, no?

effigies · 2023-11-10T21:29:58Z

Sure, why not.

stefanv · 2023-11-10T21:31:20Z

OK, so it looks like you get ninja pulled in when building via build. On scikit-image, we generate requirement.txt files from our pyproject.toml to make it easy to install build dependencies, so we need ninja there for when building the project via spin.

nipy#551 (comment)

stefanv · 2023-11-10T23:31:33Z

No, I think skimage may have done the same. We used to use it to generate requirements, but those are now picked up from the correct locations in the file.

matthew-brett · 2023-11-10T23:36:24Z

Thanks Stefan. Chris - does this look right to you now?

effigies · 2023-11-10T23:49:55Z

Yup, that all looks fine to me.

Remove setup.py information from info.py

f407de8

Shift away from info.py as source of setup information.

Allow older numpy for Python >=3.9

ee349e8

matthew-brett commented Nov 10, 2023

View reviewed changes

pyproject.toml Outdated Show resolved Hide resolved

Fix documentation URL

b4ace6a

effigies reviewed Nov 10, 2023

View reviewed changes

matthew-brett and others added 3 commits November 10, 2023 14:09

Update pyproject.toml

1c922fe

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Revert "Allow older numpy for Python >=3.9"

23bfef5

This reverts commit ee349e8, and adds some comments.

Try dropping ninja

8f513d7

matthew-brett added 2 commits November 10, 2023 21:34

Add back ninja after discussion

053fd47

nipy#551 (comment)

Delete build and default sections of optional deps

adfaf66

matthew-brett merged commit b3d202f into nipy:main Nov 11, 2023

Remove setup.py information from info.py #551

Remove setup.py information from info.py #551

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