Update examples in C and Fortran #242

atztogo · 2023-02-22T13:29:34Z

PR for #236.

simplify examples example_c and example_f
provide a conceptual example in the readme of what spglib does

The examples in C seem not so bad. So I just changed the function names of test_* to example_*.
The Fortran code of examples in Fortran was very dirty. I made it a little bit cleaner.

Conceptual examples for spg_get_dataset should be written in README.md.

Closes: #236

example/example.c

example/example_f08.f90

codecov-commenter · 2023-02-23T01:25:58Z

Codecov Report

Patch and project coverage have no change.

Comparison is base (bbb4f1e) 85.69% compared to head (86566c4) 85.69%.

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Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #242   +/-   ##
========================================
  Coverage    85.69%   85.69%           
========================================
  Files           23       23           
  Lines         6069     6069           
========================================
  Hits          5201     5201           
  Misses         868      868

Flag	Coverage Δ
c_api	`73.70% <ø> (ø)`
fortran_api	`37.37% <ø> (ø)`
python_api	`82.84% <ø> (ø)`

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atztogo · 2023-02-23T01:26:28Z

Since users in C and Fortran may be exclusive, I attempted to change directory structure and the names.

c-example/   # renamed from example/
fortran/example/  # new directory

Dependency of CMakeLists.txt files should be broken though I don't check it. Since I am afraid of conflict to modify that in upper directories, I just let it mostly unchanged.

atztogo · 2023-02-23T03:12:30Z

It is done except for CMakeLists.txt files.

LecrisUT · 2023-02-23T05:09:58Z

Since users in C and Fortran may be exclusive, I attempted to change directory structure and the names.
c-example/   # renamed from example/
fortran/example/  # new directory

I agree with that, but can it be structured like:

|-- example
  |-- c_api
  |-- fortran_api
  |-- python_api

Dependency of CMakeLists.txt files should be broken though I don't check it. Since I am afraid of conflict to modify that in upper directories, I just let it mostly unchanged.

I'll look into that. Just re-request a review to ping me when you want me to look into it.

c-example/README.md

c-example/example.c

fortran/example/README.md

c-example/example.c

fortran/README.md

fortran/example/README.md

LecrisUT · 2023-02-24T07:53:44Z

Almost done. One final thing though, why not the following folder structure:

|-- example
  |-- c_api
  |-- fortran_api
  |-- python_api

(/example/c_api, etc.)

Top example readme tells about what common minimal example is implemented in all 3 and that a complete one is also provided.

LecrisUT · 2023-02-24T10:24:57Z

Ok, my final note, fortran files should be F90 instead of f90. It's related to how they read macros and everything. It's a good standard to use.

atztogo · 2023-02-25T03:19:23Z

CI fails because CMakeLists.txts are not updated properly due to the change of directory structure and maybe f90 to F90. I think this is better treated in another PR after merging this PR and expect @LecrisUT's help.

LecrisUT · 2023-02-25T06:23:55Z

Please rebase onto develop. We cannot merge because of merge conflict.

$ git rebase origin/develop
$ git status
Check which files are conflicting and how to resolve it
$ emacs example/c_api/README.md
Command may be different because file was moved
Resolve conflicts by editting the blocks:
<<<<< HEAD
Content from origin/develop
=====
Content from branch examples
>>>>>
$ git rebase --continue

I can also recommend gitkraken if you don't feel comfortable with the git cli for this.

I will add commit fixes on top of this PR before merging when you feel it is ready.

example/fortran_api/README.md

Co-authored-by: Cristian Le <github@lecris.me>

atztogo · 2023-02-25T06:49:48Z

Please rebase onto develop. We cannot merge because of merge conflict.

Thanks for your detailed instruction. No conflict was found in rebase.

LecrisUT · 2023-02-25T06:53:14Z

Great. Pre-commit seems to fail

Oh, the merge is reporting changes from develop. A rebase would have made it cleaner to review.

atztogo · 2023-02-25T09:06:33Z

Oh, the merge is reporting changes from develop. A rebase would have made it cleaner to review.

How can I do?

LecrisUT · 2023-02-25T09:10:37Z

Oh, the merge is reporting changes from develop. A rebase would have made it cleaner to review.

How can I do?

At this point will have to interactively rebase to drop the merge commit. But basically running git rebase instead of git merge.

I'll handle that later

atztogo · 2023-02-25T09:16:04Z

At this point will have to interactively rebase to drop the merge commit. But basically running git rebase instead of git merge.

I made git rebase but when I wanted to push, git said I need to pull, and I did it with the merge way. Probably my last choice was wrong. What could I do in this case? I should force-push?

LecrisUT · 2023-02-25T09:22:15Z

https://github.com/atztogo/spglib/blob/4d66a9c249bbc96154585a01372ac8e82e41fa96/fortran/CMakeLists.txt#L2

Edit the file extension in the cmake files also.

I made git rebase but when I wanted to push, git said I need to pull, and I did it with the merge way. Probably my last choice was wrong. What could I do in this case? I should force-push?

Yes, you can freely force-push in these situations. Just never force-push the develop branch.

atztogo · 2023-02-25T09:31:05Z

Edit the file extension in the cmake files also.

Yes, I made it. e2a01d5.

atztogo · 2023-02-26T05:53:37Z

Is there anything left to do?

LecrisUT · 2023-02-26T06:14:44Z

Just to fix git history and cmake. I'll do that tomorrow

atztogo · 2023-02-26T10:23:09Z

Just to fix git history and cmake. I'll do that tomorrow

It is clearly difficult for me to do. Thanks @LecrisUT.

Signed-off-by: Cristian Le <cristian.le@mpsd.mpg.de>

LecrisUT

@atztogo I have refactored your branch and fixed the examples. I have noticed that the python example is not equivalent to the others. Could you make some changes there, and if possible add some words to example/README.md?

You can work on the same branch again by:

$ git fetch
$ git reset --hard origin/examples

Otherwise we can open a new PR for that.

And of course, thanks for all the work on this 😄

LecrisUT

Thank you fully 👍 from me. Do you want to wait for @lan496 to review as well?

atztogo · 2023-03-01T13:19:27Z

Could you make some changes there, and if possible add some words to example/README.md?

Thank you for pointing it out. I did it at ddcc153 and 86566c4.

lan496 · 2023-03-02T06:21:40Z

I have no objection. Please merge if you are ready.

atztogo · 2023-03-02T06:23:05Z

Thanks @LecrisUT and @lan496!

LecrisUT requested changes Feb 22, 2023

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LecrisUT added this to the 2.1 milestone Feb 22, 2023

atztogo changed the title ~~[WIP] Update examples in C and Fortran~~ Update examples in C and Fortran Feb 23, 2023

atztogo requested a review from LecrisUT February 23, 2023 03:11

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atztogo and others added 15 commits February 25, 2023 15:46

Update c and fortran examples

ec6e74f

Refactor example_f08.f90

f24e6ac

Change directory structure for c and fortran examples

3f9be4f

Wrote short introduction of spglib example for C

c244a58

Wrote short introduction of spglib example for Fortran

25fb04d

Update c-example/README.md

92626ea

Co-authored-by: Cristian Le <github@lecris.me>

Resolved confusing line

d4eeaed

Update fortran/example/README.md

a0f3dc5

Add comments to README.md

f3aacda

Update fortran/example/README.md

0f64153

Co-authored-by: Cristian Le <github@lecris.me>

Move conceptual examples in README.md's

e0895fe

Move c, fortran, python examples into example directory

97730d1

Fixes of example.c

57ab3ff

Renamed fortran file extensions and removed atoms.py

d878750

Update of example/fortran_api/README.md

fa8322d

atztogo and others added 3 commits February 25, 2023 15:46

Update of example/fortran_api/README.md

b2d7629

Update of fortran/README.md for writing Fortran interface design

39f848d

Update fortran/README.md

ee17c54

Co-authored-by: Cristian Le <github@lecris.me>

atztogo added 2 commits February 27, 2023 09:42

Auto-fix by mdformat

abacf62

Taking care of .F90 file names

f343e1b

LecrisUT force-pushed the examples branch from e2a01d5 to f343e1b Compare February 27, 2023 08:42

LecrisUT added 2 commits February 27, 2023 11:22

Fix the cmake and examples doumentations

7d7a0f4

Signed-off-by: Cristian Le <cristian.le@mpsd.mpg.de>

Fir example file name

14b229e

Signed-off-by: Cristian Le <cristian.le@mpsd.mpg.de>

LecrisUT approved these changes Feb 27, 2023

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LecrisUT added the documentation label Mar 1, 2023

atztogo added 2 commits March 1, 2023 22:08

Update python api examples

ddcc153

Update README.md in example directory.

86566c4

LecrisUT approved these changes Mar 1, 2023

View reviewed changes

atztogo merged commit 1d17e5e into spglib:develop Mar 2, 2023

atztogo deleted the examples branch March 2, 2023 06:22

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Update examples in C and Fortran #242

Update examples in C and Fortran #242

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Update examples in C and Fortran #242

Update examples in C and Fortran #242

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