New/sindy eq discovery

[IamShubhamGupto]

• sindy L96 equation discovery notebook
• update conda-lock file
• update index to show sindy notebook under Equation discovery with Lorenz96
• new requirements.txt file to install pip dependencies
  • conda-lock does not seem to like pip dependencies:

  •   (L96M2lines) shubham@Shubhams-MBP L96_demo % conda-lock lock --mamba -f environment.yaml -p linux-64 --kind explicit
    Locking dependencies for ['linux-64']...
    INFO:conda_lock.conda_solver:linux-64 using specs ['python 3.9.*', 'matplotlib', 'numba', 'pytorch', 'torchvision', 'scikit-learn', 'jupyter-book', 'jupyterlab', 'pre-commit', 'ffmpeg', 'tabulate', 'torch-lr-finder', 'pandas', 'conda-lock', 'pip *']
    Traceback (most recent call last):
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/src_parser/__init__.py", line 488, in seperator_munge_get
        return d[key]
    KeyError: 'matplotlib-base'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/src_parser/__init__.py", line 491, in seperator_munge_get
        return d[key.replace("-", "_")]
    KeyError: 'matplotlib_base'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/bin/conda-lock", line 10, in <module>
        sys.exit(main())
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
        return self.main(*args, **kwargs)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/core.py", line 1053, in main
        rv = self.invoke(ctx)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
        return _process_result(sub_ctx.command.invoke(sub_ctx))
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
        return ctx.invoke(self.callback, **ctx.params)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/core.py", line 754, in invoke
        return __callback(*args, **kwargs)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
        return f(get_current_context(), *args, **kwargs)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 1353, in lock
        lock_func(
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 1083, in run_lock
        make_lock_files(
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 408, in make_lock_files
        lock_content = lock_content | create_lockfile_from_spec(
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 801, in create_lockfile_from_spec
        deps = _solve_for_arch(
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 737, in _solve_for_arch
        pip_deps = solve_pypi(
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/pypi_solver.py", line 327, in solve_pypi
        src_parser._apply_categories(requested=pip_specs, planned=planned)
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/src_parser/__init__.py", line 502, in _apply_categories
        for dep in seperator_munge_get(planned, item).dependencies
      File "/Users/shubham/opt/anaconda3/envs/L96M2lines/lib/python3.9/site-packages/conda_lock/src_parser/__init__.py", line 493, in seperator_munge_get
        return d[key.replace("_", "-")]
    KeyError: 'matplotlib-base'
    

• Updated deploy.yml and preview.yml to install from conda-lock and requirements.txt, might fail due to permission issues / cannot handle pip
• Updated deploy.yml to install from conda-lock and requirements.txt

Update:

• build seems to have passed and installed all dependencies from both conda-lock and requirements.txt
• build fails near deploying pr-preview
• removed preview.yml based on our discussion below

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[dhruvbalwada]

Looks like this failed because of the same problem as #109 (which we tried to fix in #110). I hope the author can given us some useful advice.

[IamShubhamGupto]

@dhruvbalwada

it failed again for the same error, PRs from forks cannot get a preview, Im asking the authors if there's a way to go around this

Error: Resource not accessible by integration

[dhruvbalwada]

One easy solution is to give you higher level permissions on repo, would that be fine?

[IamShubhamGupto]

Hey @dhruvbalwada

Based on the reply here - rossjrw/pr-preview-action#48 (reply in thread)

The fork and pull method which we are using is not supported, I did not think of this when I was suggesting the idea.

We could:

1. Continue going without pr-previews until a solution shows up in the future
2. We get write access directly to the repository, our PRs will originate from other branches within m2lines/L96demo rather than our forks
3. As the author suggested, we use external apps like Netlify which I tried setting up for my personal project but could not figure out how to get pr-previews working, if anyone else knows, maybe they could join in and help

[dhruvbalwada]

Let's go with 1 for now, and we can figure something better out for the summer in June.

[IamShubhamGupto]

@dhruvbalwada
Sure, I am going to remove preview.yml in this branch and we should be back to how things were going before

I will be keeping requirements.txt as we now have pip dependencies