add poetry support #4754

timmysilv · 2023-10-30T14:42:05Z

Context:
Poetry helps manage dependencies in a stable way for reproducibility. PennyLane can benefit from this!

Description of the Change:
Update pyproject.toml to encapsulate the various requirements of PL grouped by task (to match the various existing requirement files). These are the details I think reviewers should consider:

TensorFlow doesn't support 3.12, but we do, so I had to hack it in with pip all over
- All docs build use the new, (mostly) auto-generated version of doc/requirements.txt instead of poetry install, but the file is more complete and stable than before
- The make lock target that I added hacks in a hard-coded tensorflow version using shell commands
- TF 2.15.0 requires ml-dtypes<0.3, but Python 3.12 requires ml-dtypes>=0.3, so that's hacked in as well
Other than the above stuff, our GitHub workflow files are much neater:) anything installed with pip (catalyst, lightning, tf) run the risk of downgrading packages. See appendix below for details on this risk
The aforementioned make lock target uses poetry to generate all files, then it changes doc/requirements.txt manually (very bad!) because docs fail with torch>=2, and it needs those TF support changes. I wouldn't read much into the requirements*.txt files other than how they're made (aka what this target calls)
I put all relevant Poetry details into the installation doc, lmk what you think
I'm not sure if I need everything in the [tool.poetry] section of pyproject.yaml, or if it should inherit from some other section later? but this worked.
I don't want to delete anything from setup.py yet, but that should come soon after this for PEP517/518 support.
I set as many minimum bounds as possible, but I can't guarantee the correctness of all of them. I often used some_pkg = "^x.y.z", which is the same as >=x.y.z,<x+1. This feels safe for explicit dependencies, but lmk what you think
cvxopt couldn't find wheels for 3.12, so I listed their links manually
sphinx is just set to ~3.5.0, but we want 4.2.0 for python 3.10+. Unfortunately, if you have 2 versions of a dependency, it will block you from exporting it to a requirements.txt file, so I removed the 4.2.0 option (because we build docs with 3.9 for now)
Poetry dependency groups are required by default, and we don't want that, so I mark them all as optional at the top

Benefits:
We can offer a more reliable and standard environment initialization in this way

Possible Drawbacks:
More complicated, might involve more maintenance. Ideally it does not, but this will depend on how we introduce and work with it. Anything installed with pip can compromise the benefits. TensorFlow, lightning, catalyst.

Appendix A - Downgrading things installed with Poetry

Today, we have jax==0.4.23 (latest) in our lockfile, but catalyst requires an earlier version (0.4.14). As you can see, it succeeds in downgrading jax, jaxlib and ml-dtypes because they were originally installed with poetry, and the new versions also fit in the range specified by pyproject.toml. Not the best because it's different from the lockfile, but not the worst because it's consistent with the toml file.

Appendix B - Downgrading things installed from requirements.txt

Because of this TF nonsense, as well as the custom sphinx action we run that expects requirements.txt, I am using that file to install all dependencies when building docs. That said, I struck a deal - the file is mostly auto-generated by poetry. However, the installation is ultimately done by pip, and that leads to an issue. In this case, the requirements file specified ml-dtypes==0.3.2 (mentioned above, multiple reasons why this had to be) and TF wanted to downgrade it. Pip raised an error, because it thought that I really, really needed 0.3.2 in all cases, even this docs CI run using python 3.9 (only 3.12 needs this). So, the make target replaces the version in the requirements file automatically.

[sc-49009]

github-actions · 2023-10-30T14:42:22Z

Hello. You may have forgotten to update the changelog!
Please edit doc/releases/changelog-dev.md with:

A one-to-two sentence description of the change. You may include a small working example for new features.
A link back to this PR.
Your name (or GitHub username) in the contributors section.

codecov · 2023-10-30T14:58:30Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (35af47f) 99.69% compared to head (eeefa5c) 99.69%.
Report is 3 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #4754   +/-   ##
=======================================
  Coverage   99.69%   99.69%           
=======================================
  Files         394      394           
  Lines       36073    36120   +47     
=======================================
+ Hits        35962    36009   +47     
  Misses        111      111

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

# Conflicts: # .github/workflows/unit-test.yml

# Conflicts: # .github/workflows/interface-unit-tests.yml

rashidnhm · 2024-01-31T20:25:27Z

requirements-ci.txt

Do we still need this file?

no, but I don't want to remove it (or any existing files) in this PR to not disturb people who might depend on it. lord knows who would other than CI (it's aptly named!) but just in case. if people are ok with deleting it, I will do that with pleasure.

rashidnhm · 2024-01-31T20:25:36Z

.github/workflows/unit-test.yml

+          pip install --upgrade pip
+          pip install --upgrade poetry wheel
+          poetry config virtualenvs.create false


I would highly recommend usage, of an action that can setup poetry. It's being used in QML as well See Here

Link to the action itself: https://github.com/XanaduAI/cloud-actions/tree/main/install-python-poetry

The benefit of using the action is that it installs poetry into a separate env to ensure poetry never attempts to manage it's own dependencies.

already a cloud-action 😍 i'll give it a shot

rashidnhm · 2024-01-31T20:36:52Z

pyproject.toml

+
+[tool.poetry]
+name = "pennylane"
+version = "0.35.0-dev"


Are we going to maintain the version of pennylane in two spots? (Pyproject + pennylane/_version.py)?

I'd rather not, but that was my short-term plan. can we have one read from the other?

So apparently the Python answer is a package should not need to know it's own version within it's own code. As there shouldn't be logic within the package itself that alters behavior using the version.

~~Now if someone decides to use the package and has logic based on version, then they can get the package version using importlib.metadata.version("{package}").~~

~~This would mean pyproject.toml being the ultimate source of truth.~~

~~Now if for backwards-compatibility reason, you want to continue to provide package.__version__, then yeah, you can have it read the pyproject.~~

I've actually done this for the Architecture team, see this: Link

You add toml as a dependency, then return the packages own version from importlib.metadata. If someone is using package in editable mode for development, then read pyproject.

EDIT: Nvm, it's still perfectly acceptable to have a version.py file .. but rather it is poetry that does not support dynamically reading the version.py file (without plugins at least).. but you can still use the link above if you'd like. Poetry Issue Link

rashidnhm · 2024-01-31T20:48:02Z

.github/workflows/docs.yml

Might be out of scope ... but can't we just drop the usage of this actions? Then use RTD's fail-on-warning configuration instead?

https://docs.readthedocs.io/en/stable/config-file/v2.html#sphinx-fail-on-warning

This way the RTD build will fail if sphinx raises a warning, which to my understanding is what this action was aimed at doing?

I don't actually know enough about this action, but I'm very open to the idea. say.. it wouldn't mind if we were using sphinx 3, would it?

I didn't know about fail on warning for RTDs! That was the main reason we had a separate action for it.

Yeah, on the PR description I see that this action is one of the reason to keep requirements-*.txt file, RTD supports poetry and pyproject just fine. Would be a cleaner solution in my opinion

well.. we can't quite use poetry alone for RTD because of tensorflow and torch issues, but that's a whole other thing : )

opened #5136 to make it happen

trbromley · 2024-02-01T14:54:14Z

doc/development/guide/installation.rst

@@ -66,6 +66,84 @@ importing PennyLane in Python.
    requires ``pip install -e .`` to be re-run in the plugin repository
    for the changes to take effect.

+Poetry


Please could we update the installation section above to recommend use of poetry?

I'm not a fan of us explicitly endorsing Poetry in this way. I think this needs to be reworded as "supports poetry" rather than explicitly want people to use this. This isn't something we'll be adding to Lightning or Catalyst, so making it an optional utility instead is what I'd prefer. Can we make this update?

mlxd

Just a quick comment. I'm still not 100% convinced poetry is better than us being fully PEP compliant, and want to make sure that is the standard first, rather than explicitly depending on Poetry. This will also influence work on Lightning and later Catalyst.

Happy to be involved in discussion around this, but I'm not sure about merging this in just yet.

mlxd · 2024-02-01T16:41:41Z

doc/development/guide/installation.rst

@@ -66,6 +66,84 @@ importing PennyLane in Python.
    requires ``pip install -e .`` to be re-run in the plugin repository
    for the changes to take effect.

+Poetry


I'm not a fan of us explicitly endorsing Poetry in this way. I think this needs to be reworded as "supports poetry" rather than explicitly want people to use this. This isn't something we'll be adding to Lightning or Catalyst, so making it an optional utility instead is what I'd prefer. Can we make this update?

timmysilv · 2024-02-01T17:15:32Z

@mlxd can you elaborate on these concerns re: lightning and catalyst? I feel like this PR should be able to remain as a standalone feature. Everything else will continue to use and be compatible with pip and the current tooling. The only thing this is really doing is using poetry to generate a lockfile, then to install the dependencies from that lockfile before running CI.

I don't feel strongly that we should recommend it to users for installation (hence the only-recent addition), and am fine to remove it. But I will say, it's a much nicer experience and if you like poetry, you might like this too. It's deep in a developer doc, but I'm good either way.

mlxd

Just a follow-on: I think as is this redefines how we are spec'ing PennyLane and adds a departure from the pip-first approach we have defaulted to elsewhere in the ecosystem we may want to rethink this.

If poetry can just be some additional helper on top of an already PEP 517/518/621 compliant package, and just does some heavy lifting in the CI, all good. If we still need to redefine parts of the project files and add all this extra machinery, I think we may want to step back from poetry for now as it may not be fit for purpose.

Let me know if making the changes isn't possible or easily done, and if not we can chat more about this with @trbromley and @Alex-Preciado as needed.

mlxd · 2024-02-02T14:30:27Z

requirements-ci.txt

+contourpy==1.2.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+cvxopt @ https://files.pythonhosted.org/packages/10/dc/1c21715e1267ca29f562e4450426d1ff8a7ffcc3e670100cec332a105b95/cvxopt-1.3.2-cp312-cp312-macosx_10_9_x86_64.whl ; sys_platform == "darwin" and platform_machine == "x86_64" and python_version == "3.12"
+cvxopt @ https://files.pythonhosted.org/packages/9f/ad/edce467c24529c536fc9de787546a1c8eca293009383a872b6f638d22eae/cvxopt-1.3.2-cp312-cp312-win_amd64.whl ; python_version == "3.12" and sys_platform == "windows"
+cvxopt @ https://files.pythonhosted.org/packages/c7/17/ee82c745c5bda340a4dd812652c42fb71efd45f663554a10c3ec45f230df/cvxopt-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ; python_version == "3.12" and sys_platform == "linux"
+cvxopt @ https://files.pythonhosted.org/packages/cd/c8/a04048143d0329ccd36403951746c1a6b5f1fc56c479e5a0a77efb2064b2/cvxopt-1.3.2-cp312-cp312-macosx_11_0_arm64.whl ; sys_platform == "darwin" and platform_machine == "arm64" and python_version == "3.12"
+cvxopt==1.3.2 ; python_full_version >= "3.9.0" and python_version < "3.12"
+cvxpy==1.4.1 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+cycler==0.12.1 ; python_version >= "3.9" and python_full_version < "4.0.0"
+ecos==2.0.12 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+fonttools==4.46.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+importlib-resources==6.1.1 ; python_version >= "3.9" and python_version < "3.10"
+kiwisolver==1.4.5 ; python_version >= "3.9" and python_full_version < "4.0.0"
+matplotlib==3.8.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+numpy==1.26.2 ; python_version >= "3.9" and python_full_version < "4.0.0"
+osqp==0.6.3 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+packaging==23.2 ; python_version >= "3.9" and python_full_version < "4.0.0"
+pillow==10.1.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+pybind11==2.11.1 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+pyparsing==3.1.1 ; python_version >= "3.9" and python_full_version < "4.0.0"
+python-dateutil==2.8.2 ; python_version >= "3.9" and python_full_version < "4.0.0"
+qdldl==0.1.7.post0 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+scipy==1.11.4 ; python_version >= "3.9" and python_full_version < "4.0.0"
+scs==3.2.4.post1 ; python_full_version >= "3.9.0" and python_full_version < "4.0.0"
+setuptools-scm==8.0.4 ; python_version >= "3.9" and python_full_version < "4.0.0"
+setuptools==69.0.3 ; python_version >= "3.9" and python_full_version < "4.0.0"
+six==1.16.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11"
+typing-extensions==4.8.0 ; python_version >= "3.9" and python_full_version < "4.0.0"
+zipp==3.17.0 ; python_version >= "3.9" and python_version < "3.10"


This is pinning packages where we didn't before. Is that necessary?

depends what you mean by necessary. Some notes on that:

as discussed in another comment, this file can be deleted altogether if we don't think people depend on it. CI doesn't use it anymore (in this PR), I just re-generated it to not delete a file that users might have counted on

the pinning is just how poetry export does it, because that's how Poetry itself behaves. You give it acceptable version ranges, it gives you one exact set of compatible versions of each dependency

I don't want to maintain both poetry and pip-style files manually - if we decide that we still have to maintain these manually for some reason, then I have some hesitations moving forward

mlxd · 2024-02-02T14:31:01Z

pyproject.toml

+[tool.poetry.group.ci.dependencies]
+cvxpy = "^1.4.1"
+cvxopt = [
+    { python = "<3.12", version = "^1.3.2" },
+    { python = "3.12", platform = "linux", url = "https://files.pythonhosted.org/packages/c7/17/ee82c745c5bda340a4dd812652c42fb71efd45f663554a10c3ec45f230df/cvxopt-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl" },
+    { python = "3.12", markers = "sys_platform == 'darwin' and platform_machine == 'x86_64'", url = "https://files.pythonhosted.org/packages/10/dc/1c21715e1267ca29f562e4450426d1ff8a7ffcc3e670100cec332a105b95/cvxopt-1.3.2-cp312-cp312-macosx_10_9_x86_64.whl" },
+    { python = "3.12", markers = "sys_platform == 'darwin' and platform_machine == 'arm64'", url = "https://files.pythonhosted.org/packages/cd/c8/a04048143d0329ccd36403951746c1a6b5f1fc56c479e5a0a77efb2064b2/cvxopt-1.3.2-cp312-cp312-macosx_11_0_arm64.whl" },
+    { python = "3.12", platform = "windows", url = "https://files.pythonhosted.org/packages/9f/ad/edce467c24529c536fc9de787546a1c8eca293009383a872b6f638d22eae/cvxopt-1.3.2-cp312-cp312-win_amd64.whl" },
+]
+matplotlib = "^3.5.0"
+
+[tool.poetry.group.doc.dependencies]
+mistune = "0.8.4"
+m2r2 = "^0.3.2"
+pygments-github-lexers = "^0.0.5"
+semantic-version = "2.10"
+docutils = "0.16"
+sphinx = "~3.5.0"  # must only provide one to export, but should be 4.2.0 for python >= 3.10
+sphinx-automodapi = "0.13"
+sphinx-copybutton = "^0.5.2"
+sphinxcontrib-bibtex = "2.4.2"
+sphinxcontrib-applehelp = "1.0.4"
+sphinxcontrib-devhelp = "1.0.2"
+sphinxcontrib-qthelp = "1.0.3"
+sphinxcontrib-htmlhelp = "2.0.1"
+sphinxcontrib-serializinghtml = "1.1.5"
+tensornetwork = "0.3"
+jinja2 = "3.0.3"
+# we do not pin the sphinx theme, to allow the
+# navbar and header data to be updated at the source
+pennylane-sphinx-theme = "*"
+sphinxext-opengraph = "0.6.3" # Note: latest version 0.9.0 requires Sphinx >=4.0
+matplotlib = "*"
+
+[tool.poetry.group.jax.dependencies]
+jax = "^0.4.14"
+jaxlib = "^0.4.14"
+
+[tool.poetry.group.torch.dependencies]
+torch = [
+    { version = "2.1.0", source = "PyPI", platform = "darwin" },
+    { version = "2.1.0+cpu", source = "pytorch-cpu", platform = "!=darwin" },
+]
+
+[tool.poetry.group.external.dependencies]
+pyzx = "^0.7.1"
+matplotlib = "*"
+stim = "*"
+
+[tool.poetry.group.qcut.dependencies]
+kahypar = "^1.1.7"
+opt_einsum = "*"
+
+[tool.poetry.group.qchem.dependencies]
+openfermionpyscf = "*"
+basis-set-exchange = "*"
+
+[tool.poetry.group.data.dependencies]
+h5py = "*"
+aiohttp = "*"
+fsspec = "*"


Is there a standard (aka non-poetry) way to handle this information in the pyproject.toml file?

from what I see, no. PEP517 and more importantly here, PEP518 are not very clear on the matter. It seems that 3P orgs can define their own 517-compliant build backend, then provide it, and that's exactly what poetry does.

mlxd · 2024-02-02T14:35:01Z

pyproject.toml

+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"


We shouldn't be converting the PEP-517 complaint build system here to be using Poetry by default.

as mentioned on your other comment, I'm not sure if it's the wrong thing to do. Poetry claims it's standard, but I'll admit that I don't know what other 517-compliant packages look like

mlxd · 2024-02-02T14:38:14Z

pyproject.toml

+"default.mixed" = "pennylane.devices.default_mixed:DefaultMixed"
+"null.qubit" = "pennylane.devices.null_qubit:NullQubit"
+"default.qutrit" = "pennylane.devices.default_qutrit:DefaultQutrit"
+


Can all poetry-specific sections here and below instead conform with the standardized PEP (e.g. 517/621/etc) ways of specifying these sections? I'd rather we didn't have poetry-specifics in something that is used to send the ecosystem out into the wild, but is only used to help manage the CI and inter-related deps therein.

Adding anything poetry specific here that becomes ingrained cannot then be used with pip/conda/etc, as it isn't standardized by Python.

I tried to change it to use non-poetry stuff locally, but poetry can only interpret its own headers. I imagine that they align for the most part, but if we intend on adding non-poetry configuration (eg. [project] instead of [tool.poetry], and [project.entry-points."pennylane.plugins"] instead of [tool.poetry.plugins."pennylane.plugins"]), there will just have to be a lot of duplication. Those cases are just s/tool.poetry/project, but that won't always be the case.

The README for their build-system makes me think that we will in fact require people to have poetry-core installed in order to pip install pennylane, but that should only be from source.

Thanks @timmysilv
I think we should discuss this more next week with @trbromley and @Alex-Preciado and see what makes the most sense here.

timmysilv · 2024-02-07T21:59:22Z

doing #5158 instead

add poetry

9769178

timmysilv added 27 commits November 16, 2023 16:46

Merge branch 'master' into use-poetry

4779eb4

remove duplicate packages from sub-groups

f3d2b58

try to not use cpu version of torch

3d9d435

try building docs with poetry

d7a3b8c

Merge branch 'master' into use-poetry

c405b59

try cpu only

3c27e81

try to use poetry for action

9f72eae

add matplotlib bc networkx dependency was implicit

1757167

put ml libraries and extras in their own groups

6a3da76

Merge branch 'master' into use-poetry

d672600

# Conflicts: # .github/workflows/unit-test.yml

more support for dependencies

5404014

put entry points in pyproject.toml

af1ef0c

readthedocs installs all groups

e31ee28

get latest packages from doc requirements file

fe392e1

Merge branch 'master' into use-poetry

3eb122a

temp: use additional_pip_packages

fdbcd67

better variable name

74e8b5c

Merge branch 'master' into use-poetry

84eb14a

# Conflicts: # .github/workflows/interface-unit-tests.yml

add mpl to external group after merge

21832cf

combine poetry install CI steps

6ac1277

install catalyst with pip to use latest jax

09f7140

bump things, notably jax

ba031b6

Merge branch 'master' into use-poetry

491590e

install aiohttp and fsspec with poetry for data/doc tests

0cef510

Merge branch 'master' into use-poetry

0edbf68

# Conflicts: # .github/workflows/interface-unit-tests.yml

bump lightning, add default.clifford

6035290

handle abstract tf tensor shapes

170565f

rashidnhm reviewed Jan 31, 2024

View reviewed changes

use poetry cloud-action

0f2e221

timmysilv mentioned this pull request Jan 31, 2024

RTD build fails on warnings, remove extra github action #5136

Closed

actually use the bin

8204aed

trbromley reviewed Feb 1, 2024

View reviewed changes

timmysilv and others added 13 commits February 1, 2024 10:06

update installation docs, try to fix CI

d49cb75

no virtualenv

aaae2c8

Resovle conflict

931f007

Add some debug stuff

e0ca9e1

Try stuff

3930dc6

Try stuff

e08832e

Try stuff

1a933c9

Try stuff

8513207

Try stuff

dc03af8

Try stuff

ad3a921

Try stuff

7f26950

Try stuff

0eb2afb

Set 'poetry run' as an env so I am calling it everywhere

308ea79

mlxd requested changes Feb 1, 2024

View reviewed changes

mlxd reviewed Feb 2, 2024

View reviewed changes

timmysilv added 4 commits February 2, 2024 12:01

revert non-venv poetry changes; use venv

120414d

bump torch

f82443a

don't hard-pin torch

c245673

Merge branch 'master' into use-poetry

eeefa5c

timmysilv closed this Feb 7, 2024

trbromley deleted the use-poetry branch February 8, 2024 14:23

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Appendix A - Downgrading things installed with Poetry

Appendix B - Downgrading things installed from requirements.txt

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timmysilv commented Feb 7, 2024

timmysilv commented Oct 30, 2023 •

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codecov bot commented Oct 30, 2023 •

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rashidnhm Jan 31, 2024 •

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