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Make pybamm_install_odes a bit more robust #3706

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agriyakhetarpal
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Description

This was a small detail that was missed; the pip install invocation inside a script should be done with a sys.executable (i.e., python/python3/python3.X) because some users' systems do not have pip added to the PATH environment variable explicitly – such as non-virtualenv-based virtual environments or those using system package managers such as apt-get or brew to manage Python dependencies This change makes it more robust and possible to work outside a virtual environment (say, if someone does not wish to use one for their own purposes, even though we strongly recommend that).

I added a --verbose command-line flag with the lowest level of verbosity possible just so that some output can be seen in the terminal, even on successful installations.

wget and cmake were added as Pythonic prerequisites to the installation guide to render the procedure clearer for users.

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

  • Bug fix (non-breaking change which fixes an issue)

Key checklist:

  • No style issues: $ pre-commit run (or $ nox -s pre-commit) (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
  • All tests pass: $ python run-tests.py --all (or $ nox -s tests)
  • The documentation builds: $ python run-tests.py --doctest (or $ nox -s doctests)

You can run integration tests, unit tests, and doctests together at once, using $ python run-tests.py --quick (or $ nox -s quick).

Further checks:

  • Code is commented, particularly in hard-to-understand areas
  • Tests added that prove fix is effective or that feature works

@agriyakhetarpal
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Tagging @Saransh-cpp, would be good to include this change into 24.1 when we are ready for that

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codecov bot commented Jan 10, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (cf2203c) 99.59% compared to head (62195f2) 99.59%.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #3706   +/-   ##
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  Coverage    99.59%   99.59%           
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  Files          258      258           
  Lines        20796    20796           
========================================
  Hits         20711    20711           
  Misses          85       85           

☔ View full report in Codecov by Sentry.
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Looks better, thanks @agriyakhetarpal

@agriyakhetarpal agriyakhetarpal merged commit c3def31 into pybamm-team:develop Jan 12, 2024
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@agriyakhetarpal agriyakhetarpal deleted the fix-pybamm-install-odes branch January 12, 2024 18:10
@agriyakhetarpal
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This one is not as essential a bug fix (since this will indeed work inside venvs) and should be fine to not go into non-RC release, but we would hope it won't break things so I would suggest its inclusion to be on the safer side of things.

Saransh-cpp pushed a commit that referenced this pull request Jan 16, 2024
Make `pybamm_install_odes` a bit more robust
Saransh-cpp pushed a commit that referenced this pull request Jan 16, 2024
Make `pybamm_install_odes` a bit more robust
rtimms added a commit that referenced this pull request May 16, 2024
* Bump to v23.9rc0

* Merge pull request #3412 from agriyakhetarpal/drop-i686-manylinux2014-support

Drop support for i686 manylinux

* Merge pull request #3413 from Saransh-cpp/improve-release-workflow

Improve release workflow, add a note, bump version manually

* Merge pull request #3436 from Saransh-cpp/fortnightly-wheels

Build wheels on the 1st and 15th of every month

* Merge pull request #3445 from pybamm-team/issue-3428-rename-exchange

#3428 exchange-current density error

* Merge pull request #3449 from pybamm-team/i3431-windows-wheels

Fix failing windows wheel builds

* Merge pull request #3456 from abillscmu/issue-3224-initial_soc

make initial soc work with half cell models

* Merge pull request #3467 from abillscmu/bugfix/initial_soh

* Merge pull request #3423 from jsbrittain/jax_gpu

JaxSolver fails when using GPU support with no input parameters

* Fix changelog

* Merge pull request #3475 from arjxn-py/fix-default-imports

Resolve default imports for optional dependencies

* Bump - `v23.9rc1`

* Fix date in CHANGELOG

* Bump version to v23.9

* Fix docs about Jax solver compatibility with Python versions (#3702)

* Ensure correct Python versions for Jax solver compatibility

* Simplify array of Python versions

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* Use different conjunction

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

---------

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* Merge pull request #3706 from agriyakhetarpal/fix-pybamm-install-odes

Make `pybamm_install_odes` a bit more robust

* #3690 fix issue with skipped steps (#3708)

* #3690 fix issue with skipped steps

* #3690 changelog

* #3690 add test

* #3611 use actual cell volume for average total heating (#3707)

* #3611 use actual cell volume for average total heating

* #3611 changelog

* #3611 account for number of electrode pairs

* #3611 update variable names

* Improve the release workflow (#3737)

* Try fixing the release workflow

* Turn off safety

* Fix CHANGELOG

* Add OS

* Use regex for better matches

* Update instructions, add safety checks

* checkout to the version branch for the final release

* Bump to v24.1rc1

* #3630 fix interpolant shape error (#3761)

* #3630 fix interpolant shape error

* #3630 changelog

* Bump to v24.1rc2

* Bump to v24.1

* Fix doctests failures in scheduled tests (#3784)

Closes #3781

* Resolve broken `scikits.odes` installation on self-hosted M-series runner (#3785)

* Try fixing M-series runner tests

This is being done by adding SuiteSparse and SUNDIALS installations which might have been missing on the runner, which broke `scikits.odes`.

* Don't use Homebrew SUNDIALS, use LD_LIBRARY_PATH

* Don't use Homebrew to install SUNDIALS

* Force remove pip cache for `scikits.odes`

---------

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* add temperature dependence to MSMR model

* changelog

* fix tests

* fix example

* rob comments

* update notebook

---------

Co-authored-by: Ferran Brosa Planella <Ferran.Brosa-Planella@warwick.ac.uk>
Co-authored-by: Saransh Chopra <saransh0701@gmail.com>
Co-authored-by: Martin Robinson <martinjrobins@gmail.com>
Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Saransh-cpp <Saransh-cpp@users.noreply.github.com>
js1tr3 pushed a commit to js1tr3/PyBaMM that referenced this pull request Aug 12, 2024
* Bump to v23.9rc0

* Merge pull request pybamm-team#3412 from agriyakhetarpal/drop-i686-manylinux2014-support

Drop support for i686 manylinux

* Merge pull request pybamm-team#3413 from Saransh-cpp/improve-release-workflow

Improve release workflow, add a note, bump version manually

* Merge pull request pybamm-team#3436 from Saransh-cpp/fortnightly-wheels

Build wheels on the 1st and 15th of every month

* Merge pull request pybamm-team#3445 from pybamm-team/issue-3428-rename-exchange

pybamm-team#3428 exchange-current density error

* Merge pull request pybamm-team#3449 from pybamm-team/i3431-windows-wheels

Fix failing windows wheel builds

* Merge pull request pybamm-team#3456 from abillscmu/issue-3224-initial_soc

make initial soc work with half cell models

* Merge pull request pybamm-team#3467 from abillscmu/bugfix/initial_soh

* Merge pull request pybamm-team#3423 from jsbrittain/jax_gpu

JaxSolver fails when using GPU support with no input parameters

* Fix changelog

* Merge pull request pybamm-team#3475 from arjxn-py/fix-default-imports

Resolve default imports for optional dependencies

* Bump - `v23.9rc1`

* Fix date in CHANGELOG

* Bump version to v23.9

* Fix docs about Jax solver compatibility with Python versions (pybamm-team#3702)

* Ensure correct Python versions for Jax solver compatibility

* Simplify array of Python versions

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* Use different conjunction

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

---------

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* Merge pull request pybamm-team#3706 from agriyakhetarpal/fix-pybamm-install-odes

Make `pybamm_install_odes` a bit more robust

* pybamm-team#3690 fix issue with skipped steps (pybamm-team#3708)

* pybamm-team#3690 fix issue with skipped steps

* pybamm-team#3690 changelog

* pybamm-team#3690 add test

* pybamm-team#3611 use actual cell volume for average total heating (pybamm-team#3707)

* pybamm-team#3611 use actual cell volume for average total heating

* pybamm-team#3611 changelog

* pybamm-team#3611 account for number of electrode pairs

* pybamm-team#3611 update variable names

* Improve the release workflow (pybamm-team#3737)

* Try fixing the release workflow

* Turn off safety

* Fix CHANGELOG

* Add OS

* Use regex for better matches

* Update instructions, add safety checks

* checkout to the version branch for the final release

* Bump to v24.1rc1

* pybamm-team#3630 fix interpolant shape error (pybamm-team#3761)

* pybamm-team#3630 fix interpolant shape error

* pybamm-team#3630 changelog

* Bump to v24.1rc2

* Bump to v24.1

* Fix doctests failures in scheduled tests (pybamm-team#3784)

Closes pybamm-team#3781

* Resolve broken `scikits.odes` installation on self-hosted M-series runner (pybamm-team#3785)

* Try fixing M-series runner tests

This is being done by adding SuiteSparse and SUNDIALS installations which might have been missing on the runner, which broke `scikits.odes`.

* Don't use Homebrew SUNDIALS, use LD_LIBRARY_PATH

* Don't use Homebrew to install SUNDIALS

* Force remove pip cache for `scikits.odes`

---------

Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* add temperature dependence to MSMR model

* changelog

* fix tests

* fix example

* rob comments

* update notebook

---------

Co-authored-by: Ferran Brosa Planella <Ferran.Brosa-Planella@warwick.ac.uk>
Co-authored-by: Saransh Chopra <saransh0701@gmail.com>
Co-authored-by: Martin Robinson <martinjrobins@gmail.com>
Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Saransh-cpp <Saransh-cpp@users.noreply.github.com>
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2 participants