Conda packaging by AurelienBesnier · Pull Request #131 · openalea/hydroshoot

AurelienBesnier · 2025-05-20T15:16:00Z

Just an update of the conda packaging with the new versioning system

add blank line at the end of the file

Add blank line

pradal · 2025-05-20T15:31:26Z

conda/meta.yaml

+{% set home = pyproject.get('project', {}).get('urls', {}).get('Homepage', '') %}
+{% set build_deps = pyproject.get("build-system", {}).get("requires", []) %}
+{% set deps = pyproject.get('project', {}).get('dependencies', []) %}
+{% set conda_deps = pyproject.get('tool', {}).get('conda-environment', {}).get('dependencies',[]) %}


Here conda-dependencies are note set.
Perhaps adding them to pyproject.yaml

pradal · 2025-05-20T15:32:29Z

conda/meta.yaml

-    - pandas
-    - jsonschema
-    - pvlib-python
    - openalea.mtg


need to move this to pyproject.toml

pradal · 2025-05-20T15:33:15Z

conda/meta.yaml

-    - pvlib-python
    - openalea.mtg
    - openalea.plantgl
    - alinea.caribu


Replace alinea.caribu and alinea.astk by one new version.
But perhaps in another PR

… conda_packaging

pradal

You also may change the pyproject.toml for management of the version.
See the documentation (https://openalea.rtfd.io)

pradal · 2025-09-04T15:03:14Z

in pyproject.toml

[tool.setuptools_scm]
# Format version to ease alignment with conda/meta.yaml tag-based versioning
fallback_version = "0.0.0.dev0"
version_scheme = "guess-next-dev"
local_scheme = "no-local-version"

RamiALBASHA · 2025-09-04T15:07:28Z

Thanks for the updates.
There are still two failed jobs :

cannot find alinea.caribu dependecy : https://github.com/openalea/hydroshoot/actions/runs/17382250925/job/49575905207?pr=131#step:3:1342
compatibility issue https://github.com/openalea/hydroshoot/actions/runs/17382250925/job/49575905240?pr=131#step:3:3759

thanks again

AurelienBesnier · 2025-09-04T15:16:30Z

Thanks for the updates. There are still two failed jobs :

* cannot find alinea.caribu dependecy : https://github.com/openalea/hydroshoot/actions/runs/17382250925/job/49575905207?pr=131#step:3:1342

* compatibility issue https://github.com/openalea/hydroshoot/actions/runs/17382250925/job/49575905240?pr=131#step:3:3759

thanks again

No problems ! For the alinea.caribu problem it should solve itself once caribu is available for osx-arm64
For the compatibility issue, we are working on it in openalea/plantgl#80

pradal

Few comments but they are quite general and not specific to hydroshoot

pradal · 2025-09-04T19:26:14Z

.github/workflows/conda-package-build.yml

-    uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
+    uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
    secrets:
      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}


add end of line

pradal · 2025-09-04T19:28:20Z

conda/meta.yaml

-    - setuptools
+  host:
+    - python
+    {% for dep in build_deps %}


need setuptools_scm
but other build_deps are not host, isn't it?
If so we need to change the doc and all the packages

pradal · 2025-09-04T19:32:16Z

pyproject.toml

  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",


We can also add "Framework :: OpenAlea"

pradal · 2025-09-04T19:33:47Z

pyproject.toml

+# enable dynamic version based on git tags
+[tool.setuptools_scm]
+# Format version to ease alignment with conda/meta.yaml tag-based versioning
+fallback_version = "0.0.0.dev0"


perhaps the latest version 5.2.2? Rather than 0.0.0

christian34 · 2025-09-08T13:31:24Z

The bug on windows is just because alinea.caribu is too old : the caribu PR should be accecpted first (one maclatest is okay !)

pradal · 2025-09-17T07:42:53Z

We need to move on for the release.
Can you review and merge this PR?
Or give us the green light, and we will maintain it.

pradal · 2025-10-23T12:12:31Z

@RamiALBASHA : a gentle reminder.
If you have some difficulty on merging it, we can discuss

RamiALBASHA

Thanks for this improvement @pradal , @AurelienBesnier.
I have some questions:

Is it possible to make an editable installation using pip? I installed the package using mamba as indicated in the README and the installation ran without any error. HydroShoot was then installed as a dependency in my mamba env.
However, performing pip install -e . fails:

      ERROR: Could not find a version that satisfies the requirement setuptools (from versions: none)
      ERROR: No matching distribution found for setuptools

How can we now develop the package without an editable installation?

how dependencies are handleded? the optional dependencies are not installed with mamba, which is logic. However, if I cannot perform a manual installation (pip install .), how can I then use pyproject.toml? (same pblm as above)
Is the version now hard-coded in pyproject.toml? Just to verify, since I'm not familiar yet with setuptools_scm

pradal · 2025-10-23T14:13:31Z

Hi Rami!

Editable version: Yes. This is how all the docs are built. We install all the deps and then we run pip install -e .
This is working very well for pure Python pkgs. And we are working on it for compiled models (like caribu or plantgl)

But we do that on a mamba environment where the deps have been installed.
If it is not clear, I will update the doc

If you are a developper, you install the deps with mamba. And your package with pip in this mamba env
No. The version is infered from the tag. All the release pipeline is driven by the tags

RamiALBASHA · 2025-10-23T14:18:34Z

Editable version: Yes. This is how all the docs are built. We install all the deps and then we run pip install -e .
This is working very well for pure Python pkgs. And we are working on it for compiled models (like caribu or plantgl)

If you are a developper, you install the deps with mamba. And your package with pip in this mamba env

@pradal So should I extract the deps from pyproject.toml and put them into some requirements.txt and make dependencies dynamic now in pyproject.toml?

If it is not clear, I will update the doc

thanks, yes

No. The version is infered from the tag. All the release pipeline is driven by the tags

The workflow obliges now to release a new tag each time the devs want to bump the version? (just to understand)

pradal · 2025-10-23T14:24:56Z

We add an environment.yaml in conda (see https://github.com/openalea/hydroroot/blob/main/conda/environment.yml)

So you can build the env with

mamba env -f conda/environment.yaml

RamiALBASHA · 2025-10-23T15:05:15Z

@pradal
I have tried mamba env create -f conda/environment.yml -n MyEnv and got:

PackagesNotFoundError: The following packages are not available from current channels:

  - openalea.caribu

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/openalea3

Should we merge this PR now and open an issue for editable installation, or wait until the compiled libraries are handled?

pradal · 2025-10-23T15:09:08Z

Yes. Sure.

You need to add

-c openalea3/label/dev -c openalea/label/rc -c openalea3 -c conda-forge

RamiALBASHA · 2025-10-23T17:56:06Z

@pradal
mamba env create doesn't accept -c flags for channels directly in the command line.
I added the channels to environment.yml as:

channels:
  - conda-forge
  - openalea3
  - openalea3/label/dev
  - openalea/label/rc

but hit a new problem:

package openalea.caribu-8.1.4.dev-py3.13 requires python >=3.13,<3.14.0a0, but none of the providers can be installd

pradal · 2025-10-23T18:51:59Z

Sure
I recommend you to add the same channels but with another priority:

channels:
  - openalea3/label/dev
  - openalea/label/rc
  - openalea3
  - conda-forge

A package is first uploaded to dev when the branch is merge in the master or main branch .
Then when a tag is added, the pkg move to rc.
And when the package is released, it will move to openlea3

Otherelse, this is stange that there are conflicts.

pradal · 2025-11-05T16:43:06Z

Hi @RamiALBASHA
I fix the error in conda/environment.yml

Just by running

mamba env -f conda/environment.yml

Everything is installed and work. I suucced to run some examples.

BESNIER AURELIEN and others added 3 commits May 20, 2025 17:01

Better conda-packaging

e38a66b

fixing ci parameter name

a3cd567

Removing unused version file

f1fa09e

AurelienBesnier linked an issue May 20, 2025 that may be closed by this pull request

Conda Packaging (meta.yaml) #130

Closed

pradal requested review from RamiALBASHA and pradal May 20, 2025 15:27

pradal added 2 commits May 20, 2025 16:34

Update __init__.py

f224bde

add blank line at the end of the file

Update environment.yml

2cfbf48

Add blank line

pradal reviewed May 20, 2025

View reviewed changes

AurelienBesnier added 2 commits May 22, 2025 09:50

Updating conda deps

a0bfb30

Merge branch 'conda_packaging' of github.com:openalea/hydroshoot into…

635d1e2

… conda_packaging

pradal approved these changes May 23, 2025

View reviewed changes

AurelienBesnier added 5 commits September 1, 2025 17:38

Update github action

d0ff782

Update conda section

d44d595

Update meta.yaml to guidelines

e214a3a

Update dev package name

95a1a04

Adding missing build string

fb656fe

pradal reviewed Sep 4, 2025

View reviewed changes

Update pyproject.toml for version management

67498e0

pradal approved these changes Sep 4, 2025

View reviewed changes

AurelienBesnier added 3 commits September 5, 2025 09:38

Update pyproject.toml Framework + fallback_version

743f62a

Adding setuptools_scm

aa91936

Adding eol

b138d15

pradal approved these changes Sep 5, 2025

View reviewed changes

Using openalea.caribu

608f2c1

RamiALBASHA reviewed Oct 23, 2025

View reviewed changes

fix errors in environment.yml

ffe774a

RamiALBASHA merged commit 609f5df into master Dec 2, 2025
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