Z2pack with elk

[euclidmenot2]

The kpoints.py file was modified to add an interface to Elk, an all-electron DFT code (http://elk.sourceforge.net/). Example Elk and Z2Pack input files for Bi2Se3 were also added.

[codecov[bot]]

Codecov Report

Merging #112 (6b1bd5c) into dev/current (a87eee5) will decrease coverage by 1.39%. The diff coverage is 14.81%.

:exclamation: Current head 6b1bd5c differs from pull request most recent head 284b57c. Consider uploading reports for the commit 284b57c to get more accurate results

@@               Coverage Diff               @@
##           dev/current     #112      +/-   ##
===============================================
- Coverage        93.36%   91.96%   -1.40%     
===============================================
  Files               37       37              
  Lines             1492     1519      +27     
===============================================
+ Hits              1393     1397       +4     
- Misses              99      122      +23     

Impacted Files	Coverage Δ
z2pack/fp/kpoint.py	84.00% <14.81%> (-15.19%)	:arrow_down:

---

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[greschd]

Hi @euclidmenot2,

First off, thanks for taking the time to contribute!

It seems there are some problems with the pre-commit hooks. Instead of running them through continuous integration for every change, it is much quicker to run them locally. You can follow the following steps (some of which you may have already done):

• clone the repository: [email protected]:euclidmenot2/Z2Pack.git
• go into the Z2Pack directory: cd Z2Pack
• check out the correct branch: git checkout z2packWithElk
• create a virtual environment in which to install Z2Pack (instructions differ depending on which method you prefer, e.g. conda or virtualenv)
• Install Z2Pack with development dependencies pip install -e .[dev]
• Activate the pre-commit hooks: pre-commit install
• Run the hooks: pre-commit run --all-files

The last command should automatically format the code, and run the other style checkers.

Once you're done:

• Add the code: git add --all
• Check which files were added with git status
• Commit the code, and push: git commit; git push

Let me know if that works for you, or you're stuck somewhere. Unfortunately we don't have a comprehensive contributing guide that would cover these things.

[euclidmenot2]

Hi Dr. Gresch,

Thank you! I'm very new to github (mostly an experimentalist who only recently ventured into computation). I'm now getting though the pre-commit and tests sections successfully. I now seem to be having issues with Codecov regarding test coverage.

[image: image.png]

[image: image.png] I think that this means that I need to write some new tests for the Elk portion. When I try to upload my Bi2Se3 Elk output files, some of the files are larger than 25 MB, the Github limit. I am going to start running some test calculations for Bi, hoping that the output files will be smaller but, as it currently stands, this may be a limiting factor. Would you have some guidance?

Thanks, Lisa Pogue

Postdoc McQueen Laboratory Johns Hopkins University

On Thu, Mar 25, 2021 at 1:23 PM Dominik Gresch @.***> wrote:

Hi @euclidmenot2 https://github.com/euclidmenot2,

First off, thanks for taking the time to contribute!

It seems there are some problems with the pre-commit hooks. Instead of running them through continuous integration for every change, it is much quicker to run them locally. You can follow the following steps (some of which you may have already done):

• clone the repository: @.***:euclidmenot2/Z2Pack.git
• go into the Z2Pack directory: cd Z2Pack
• check out the correct branch: git checkout z2packWithElk
• create a virtual environment in which to install Z2Pack (instructions differ depending on which method you prefer, e.g. conda or virtualenv)
• Install Z2Pack with development dependencies pip install -e .[dev]
• Activate the pre-commit hooks: pre-commit install
• Run the hooks: pre-commit run --all-files

The last command should automatically format the code, and run the other style checkers.

Once you're done:

• Add the code: git add --all
• Check which files were added with git status
• Commit the code, and push: git commit; git push

Let me know if that works for you, or you're stuck somewhere. Unfortunately we don't have a comprehensive contributing guide that would cover these things.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Z2PackDev/Z2Pack/pull/112#issuecomment-807135542, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO6BZQ2UYQ2CHFC6TYFY74TTFNWSRANCNFSM4ZZV3U7A .

[greschd]

Great! Yes, the codecov check tests for whether the changed code was covered by tests. In principle we can override it if needed, but it would be indeed good to have some tests.

Indeed, the Elk output files probably shouldn't be committed to the repository. Still, there are some ways in which we can add tests - following what is done for the other first-principles codes. There are two kinds of test:

• The tests for the k-point function, located here: https://github.com/Z2PackDev/Z2Pack/blob/dev/current/tests/fp/test_fp_kpoint.py. These should be possible to add also with elk. When you add new tests there, it will create files with a "reference" the first time that is run. That can be inspected for correctness, and committed to the repository if it is ok.

• Full tests, which run the first-principles code. Currently, the setup is such that they can only be run locally. This is a bit sub-optimal, but I haven't yet taken on the complexity of getting the codes themselves to run in CI. You can see an example at https://github.com/Z2PackDev/Z2Pack/blob/dev/current/tests/fp/test_espresso_new.py. There's even a hard-coded path to the code in there... something which I should fix. For now, you can do the same for Elk.

  There is a helper compare_wcc which checks that the WCC result does not change after the first time it has run. Again, the idea is to manually check that the first-principles "plugin" works, and then validate that it keeps working with the test.

  The tests are "marked" https://github.com/Z2PackDev/Z2Pack/blob/a87eee59753be0b08c43a124a1690ceafeb3cce9/tests/fp/test_espresso_new.py#L65 which means these tests will be skipped unless the --quantumespresso flag is passed to the test run. These markers are defined in conftest.py: https://github.com/Z2PackDev/Z2Pack/blob/a87eee59753be0b08c43a124a1690ceafeb3cce9/tests/conftest.py#L21-L25

  https://github.com/Z2PackDev/Z2Pack/blob/a87eee59753be0b08c43a124a1690ceafeb3cce9/tests/conftest.py#L39-L41

  The same kind of marker can be added for Elk.

The tests can be executed by running pytest from the root of the project, or with a specific test file as argument (e.g. pytest tests/fp/test_fp_kpoint.py).

Hope this gets you a step further, happy to help out if you're running into problems. -Dominik

[euclidmenot2]

Hi Dominik,

I am still having issues with Github and codecov on my Windows machine (I run my calculations on a separate Linux cluster that I do not run Github on). When I try to clone Z2pack using the Github Desktop app on my Windows machine, I get clone errors:

My workaround was to download as a *.zip, modify the files, run pylint and yapf, then re-upload. However, I haven't been able to get codecov to work with this workaround. Would you have any advice?

Thanks,

Lisa

Note: I now have the new Conda environment installed with the elk development version of Z2pack. However, I am not in a Git repository because of the aforementioned issues. It now won't let me activate and the pre-commit hooks. I could use some help when it comes to pushing the changes since the Github cloning seems to be having some issues.

Lisa

[euclidmenot2]

To elaborate more, with my *.zip work-around, when I update test_fp_kpoint.py. and then re-upload it with an elk valid_lines (the VASP valid lines with a few name changes), it doesn't seem as though the reference data is being created (I am getting "Reference data does not exist value errors). I think that this is happening since I am using Continuous Integration and might be avoided if I could get Git to work nicely with Windows. Would you have any advice? I'm now trying to track down a Linux machine that is not our cluster.

Thanks again, Lisa

[greschd]

Hi Lisa,

I think the reason you're getting the "Reference data does not exist" errors is that this "reference data" should be added to the .pytest_cache/v directory: https://github.com/Z2PackDev/Z2Pack/tree/dev/current/.pytest_cache/v

When you run the tests locally, these files are generated the first time you run them. Note that not the entire .pytest_cache directory should be added, only the test_<test_name> directories.

The reason why these files need to be added is that we make use of the "caching" feature in pytest to store reference data. The pytest-regressions package would be a better way of doing this, but I haven't gotten around to migrating this yet.

It seems the error you're getting in the git GUI is also somehow related to the .pytest_cache directory, although I can't quite figure out from the screenshot what is wrong.

Finally, if you need access to a Linux system on your Windows machine, you could try the "Windows Subsystem for Linux": https://docs.microsoft.com/en-us/windows/wsl/

Dominik