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Cannot run tutorial after active papers installation #20
Comments
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The "data not extractable" messages are expected. "aptool checkout" is meant for code and documentation, and can in fact only handle text. Anything labelled "data" is an HDF5 dataset. It doesn't have an obvious on-disk representation that could be checked out. Accessing the data thus requires HDF5. The ActivePaper file is an HDF5 file, so you can open it using |
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Nevertheless, |
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So the big question is: what's different between our environments? Guix has 214 dependencies of ActivePapers, but that's because it includes all compile-time tools, recursively. Picking from that list the packages you have listed above, as much as possible, I find: Lots of small differences, nothing that looks obviously problematic. |
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Looking at your traceback, what strikes me is the file name Could you check what the file `activepapers/version.py' contains in your environment? |
Ah, I also tried the PyPI ActivePapers version, and I copy-pasted the wrong traceback. Now edited. But it doesn't look different.
What I would expect is either:
A list of zero-byte files is not what I expected.
It's a bit scary to have scientific data hidden from non-programmers. If you wish, I could cook up an extract data script that does the equivalent of |
This is the best I can do in order to match your package versions: name: active-papers
channels:
- conda-forge
dependencies:
- python=3.9
- pip
- hdf5=1.10
- numpy==1.21
- pip:
- h5py==3.6.*
- tempdir==0.7.*
- matplotlibNo difference in the traceback EDIT: better matching of the package versions |
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I agree about data checkout, and opened an issue for that (#21). Thanks for trying to match my versions! This still looks weird. I'll have to debug this under Miniconda. |
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Active papers installation
Environment
active_papers.ymlInstallation commands
mamba env create --file active-papers.yml conda activate active-papers git clone https://github.com/activepapers/activepapers-python cd activepapers-python python3 setup.py installInstalled packages
Output:
Running the tutorial
Output:
ls -l `find data -type f -name '*'`Output:
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