Comments (7)
With poetry we probably want to make the rnn dependencies optional, as they are quite heavy (mainly tensorflow).
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Another todo: generate the documentation, and probably for that to work we have to pick one convention for docstrings as currently we're using different ones.
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I manually updated pyproject.toml adding the rnn dependencies. For the versions I checked what the latest was and used that, but that might not be necessary. Then ran poetry lock --no-update
to add these to the lock file without upgrading versions of other packages. Then tested installing with poetry install
, but there is an issue with tensorflow, specifically: Unable to find installation candidates for tensorflow-io-gcs-filesystem (0.27.0) (related issue)
Likely this is because I'm on a (arm) mac, replacing tensorflow with tensorflow-macos fixed it for me, everything now installs. But this needs to be fixed for everyone somehow..
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It runs now, as long as the data is present at grainlearning/rnn/data/sequences.hdf5
. Wandb creates a folder inside rnn/
.
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We picked the following convention for docstrings:
- Use python type hints.
- Use sphinx format for docstrings, specifically:
:param : and :return :, we are dropping :type : and :rtype:
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Regarding the dependencies, In this commit I created two groups of extras rnn and rnn_M1_macOS with the necessary dependencies (only difference is in tensorflow).
I tested in my machine poetry install -E rnn_M1_macOS
and on Snellius poetry install -E rnn
, and the dependencies are handled correctly.
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The installation of tensorflow for arm64 macOS requires some extra steps that cannot be handled from poetry. I think the best is to keep it separately: if an user has M1 macOS he/she will have to install tensorflow first on his own, and then he/she can install grainLearning on the same python environment.
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Related Issues (20)
- Improve test coverage HOT 1
- Documentation build is failing HOT 1
- Refactor CalibrationToolBox class (now called GrainLearning) HOT 1
- Correlation metrics among other data analytics tools
- Change relative import to absolute imports everywhere in grainlearning
- Generalization of RNN module
- in Windows wandb doesn't generate latest-run HOT 3
- Add possibility to have multiple control variables
- Feedback on GrainLearning from Balazs HOT 1
- Update Python version to 3.12
- Maintenance of poetry.toml
- Unwanted persistance in interative notebooks HOT 1
- Error handling in invalid simulations
- Improving callback functions HOT 2
- IODynamicClass redundant init variables HOT 1
- Remove python version 3.8 from workflows and released wheels HOT 2
- RNN integration to GL
- Make predictions using only input and param data
- Automatically run a hyperparameter tuning HOT 3
- JOSS Review: Paper Comments HOT 7
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