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Fix the failing CI and docs #161

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Fix the failing CI and docs #161

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Saransh-cpp
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The CI is failing with an error -

File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/ray/__init__.py", line 108, in <module>
    import ray._raylet  # noqa: E402
  File "python/ray/_raylet.pyx", line [115](https://github.com/pybamm-team/liionpack/runs/6735663537?check_suite_focus=true#step:8:116), in init ray._raylet
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/ray/exceptions.py", line 7, in <module>
    from ray.core.generated.common_pb2 import RayException, Language, PYTHON
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/ray/core/generated/common_pb2.py", line 15, in <module>
    from . import runtime_env_common_pb2 as src_dot_ray_dot_protobuf_dot_runtime__env__common__pb2
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/ray/core/generated/runtime_env_common_pb2.py", line 36, in <module>
    _descriptor.FieldDescriptor(
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/google/protobuf/descriptor.py", line 560, in __new__
    _message.Message._CheckCalledFromGeneratedFile()
TypeError: Descriptors cannot not be created directly.
If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0.
If you cannot immediately regenerate your protos, some other possible workarounds are:
 1. Downgrade the protobuf package to 3.20.x or lower.
 2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).
More information: https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates

The error originates from a breaking change in the new protobuf release which is used by ray. Ray has fixed this on the development branch but hasn't tagged a new version yet, see' - ray-project/ray#25282.

The docs are failing with a weird issue related to site.py (here is a thread on this - pypa/virtualenv#737) -

Collecting pybamm
  Downloading pybamm-22.4.tar.gz (908 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 908.2/908.2 kB 263.4 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [17 lines of output]
      running egg_info
      creating /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info
      writing /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/PKG-INFO
      writing dependency_links to /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/dependency_links.txt
      writing entry points to /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/entry_points.txt
      writing requirements to /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/requires.txt
      writing top-level names to /tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/top_level.txt
      writing manifest file '/tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/SOURCES.txt'
      reading manifest file '/tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/SOURCES.txt'
      adding license file 'LICENSE.txt'
      writing manifest file '/tmp/pip-pip-egg-info-7u9fhlpe/pybamm.egg-info/SOURCES.txt'
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-qcqekzwj/pybamm_df8f00e690954098bc64a5e92bd1d207/setup.py", line 227, in <module>
          path_to_sitepackages = site.getsitepackages()[0]
      AttributeError: module 'site' has no attribute 'getsitepackages'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

The docs are using PyBaMM version 22.4, which might be an issue? If not then the virtual environment would have to be checked.

This PR also changes the old parameter style to the new refactored one!

@Saransh-cpp
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Can we now not do parameter_values.evaluate(param.n.c_init)? This gives a pybamm related error -

    C_n = parameter_values.evaluate(param.n.c_init)
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/pybamm/parameters/parameter_values.py", line 765, in evaluate
    return processed_symbol.evaluate()
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/pybamm/expression_tree/unary_operators.py", line 74, in evaluate
    return self._unary_evaluate(child)
  File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/pybamm/expression_tree/unary_operators.py", line 59, in _unary_evaluate
    raise NotImplementedError(
NotImplementedError: <class 'pybamm.expression_tree.broadcasts.FullBroadcast'> does not implement _unary_evaluate.

@TomTranter
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Hi @Saransh-cpp thanks for raising this PR. I think the problem is that the variables got slightly redefined. I have another PR that fixes this issue using param.n.cap_init and it has other changes in too. I think might be simpler for me to make the protobuf change and setup.py change in that branch and close this one

@TomTranter
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@Saransh-cpp my ci build on github seems to be working but if I login to readthedocs and manually build the branch I get an error. Seems like ray is re-installing the latest protobuf

https://readthedocs.org/api/v2/build/17139080.txt

@Saransh-cpp
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I think might be simpler for me to make the protobuf change and setup.py change in that branch and close this one

Yes, makes sense! I'll close this one up

For the RTD error, I found this in the logs -

[rtd-command-info] start-time: 2022-06-09T14:20:49.718580Z, end-time: 2022-06-09T14:21:04.171368Z, duration: 14, exit-code: 0
/home/docs/checkouts/readthedocs.org/user_builds/liionpack/envs/issue_158_fix_build/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs]
Processing /home/docs/checkouts/readthedocs.org/user_builds/liionpack/checkouts/issue_158_fix_build
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
WARNING: liionpack 0.3.1 does not provide the extra 'docs'
Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/liionpack/envs/issue_158_fix_build/lib/python3.8/site-packages (from liionpack==0.3.1) (1.22.4)
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Collecting setuptools>=18.5
  Downloading setuptools-62.3.3-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 20.4 MB/s eta 0:00:00
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Building wheels for collected packages: liionpack
  Building wheel for liionpack (setup.py): started
  Building wheel for liionpack (setup.py): finished with status 'done'
  Created wheel for liionpack: filename=liionpack-0.3.1-py3-none-any.whl size=31500 sha256=9e4cd61cf5fa6e083e2fcc65ea5d5965aa118efcfab66a2c43fbfa0657d6daab
  Stored in directory: /tmp/pip-ephem-wheel-cache-lh7l316y/wheels/0d/d7/69/c2ef746b9bdc00eb25aa3a7b4307278bcd532fd9ada40f0191
Successfully built liionpack
Installing collected packages: setuptools, protobuf, liionpack
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.2.0
    Uninstalling setuptools-58.2.0:
      Successfully uninstalled setuptools-58.2.0
  Attempting uninstall: protobuf
    Found existing installation: protobuf 3.20.1
    Uninstalling protobuf-3.20.1:
      Successfully uninstalled protobuf-3.20.1
Successfully installed liionpack-0.3.1 protobuf-4.21.1 setuptools-62.3.3

RTD is running python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs] which is forcing every dependency, including protobuf to be upgraded. Is it possible to change this command after logging in?

@Saransh-cpp Saransh-cpp closed this Jun 9, 2022
@TomTranter TomTranter deleted the fix-tests branch July 1, 2022 11:46
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@Saransh-cpp @TomTranter