Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` #4021

DanielYang59 · 2024-08-28T13:17:33Z

Summary

Replace HTTP URLs with HTTPS
Replace some expired URLs
Avoid from pytest import raises/mark (a bit unsure about MonkeyPatch so just use pytest.MonkeyPatch if pytest is already imported)
Regenerate documents

DanielYang59 · 2024-08-28T13:20:11Z

src/pymatgen/io/abinit/abiobjects.py

@@ -56,7 +56,7 @@ def lattice_from_abivars(cls=None, *args, **kwargs):
            raise ValueError(f"The sum of angdeg must be lower than 360, {ang_deg=}")

        # This code follows the implementation in ingeo.F90
-        # See also http://www.abinit.org/doc/helpfiles/for-v7.8/input_variables/varbas.html#angdeg


I have to replace this with the latest doc (doesn't seem to be versioned) instead of the original v7.8, because the original URL seems inaccessible.

DanielYang59 · 2024-08-28T13:50:45Z

@janosh Please review this. Looks like we might need to regenerate docs, thanks!

I reverted the rebuild doc commit because it makes it impossible to review. Would let you do this, appreciate that!

This reverts commit 47e4d59.

janosh · 2024-08-28T14:23:20Z

Currently on my phone. Could you apply the docs commit again?

src/pymatgen/io/exciting/inputs.py

DanielYang59 · 2024-08-29T02:05:42Z

src/pymatgen/alchemy/materials.py

@@ -369,7 +369,7 @@ def to_snl(self, authors: list[str], **kwargs) -> StructureNL:
            history += [
                {
                    "name": snl_metadata.pop("name", "pymatgen"),
-                    "url": snl_metadata.pop("url", "http://pypi.python.org/pypi/pymatgen"),
+                    "url": snl_metadata.pop("url", "https://pypi.python.org/pypi/pymatgen"),


This might potentially be a breaking change too (already reverted), the metadata (default value of pop for url would have been changed):

pymatgen/src/pymatgen/alchemy/materials.py

Lines 367 to 375 in 46d843c

for hist in self.history:

snl_metadata = hist.pop("_snl", {})

history += [

{

"name": snl_metadata.pop("name", "pymatgen"),

"url": snl_metadata.pop("url", "http://pypi.python.org/pypi/pymatgen"),

"description": hist,

}

]

janosh

ideally, we should have a link checker CI similar to pymativz to make sure all the new (and old links) are actually still alive. but i'm happy to leave that to a future PR. maybe something to open an issue for so it's not forgotton

DanielYang59 · 2024-08-30T05:42:53Z

ideally, we should have a link checker CI similar to pymativz to make sure all the new (and old links) are actually still alive. but i'm happy to leave that to a future PR. maybe something to open an issue for so it's not forgotton

Wonderful. Added to my TODO list (which is not very long at this moment :) ). I would need some investigation on that because markdown-link-check seemingly just check markdown files.

Can you regenerate documents after reviewing? Thanks!

janosh · 2024-08-30T05:49:56Z

@DanielYang59 do you want to reapply the docs update commit before i merge?

DanielYang59 · 2024-08-30T05:55:25Z

@janosh certainly, got two warnings at the start, not sure if we should worry about that or not (it seems favicon.ico and html_static_path = ["assets"] don't exist?):

>>> invoke make-doc
rm: pymatgen.*.rst: No such file or directory
Running Sphinx v7.4.7
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry 'assets' does not exist
WARNING: favicon file 'favicon.ico' does not exist
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 49 source files that are out of date
updating environment: [new config] 49 added, 0 changed, 0 removed

janosh · 2024-08-30T06:01:18Z

@janosh certainly, got two warnings at the start, not sure if we should worry about that or not (it seems favicon.ico and html_static_path = ["assets"] don't exist?):

safe to ignore for now. the docs need some more work at some point but that would be a bigger project

DanielYang59 · 2024-08-30T06:03:38Z

Great to know! Thanks.

DanielYang59 added 7 commits August 28, 2024 20:49

replace http with https, all committed changes verified

ec781a4

replace more http with https

3cdaac2

replace expired abinit urls

96a4de7

replace scipy expired url

8b61e34

update NIST url and w3.org

1699abe

update netCDF4 doc url

1467780

replace some http with https in unit test

a8f4f1b

DanielYang59 commented Aug 28, 2024

View reviewed changes

remove debug leftover

de73948

DanielYang59 changed the title ~~Replace http URLs with https~~ Replace HTTP URLs with HTTPS Aug 28, 2024

DanielYang59 marked this pull request as ready for review August 28, 2024 13:27

DanielYang59 requested review from shyuep, janosh and mkhorton as code owners August 28, 2024 13:27

DanielYang59 added 4 commits August 28, 2024 21:53

add missing build doc dependency

33917f9

rebuild docs

47e4d59

add invoke to docs dependency

8ee24c1

Revert "rebuild docs" as it makes it impossible to review

0445dcf

This reverts commit 47e4d59.

janosh approved these changes Aug 28, 2024

View reviewed changes

DanielYang59 commented Aug 28, 2024

View reviewed changes

src/pymatgen/io/exciting/inputs.py Outdated Show resolved Hide resolved

revert replace on io.exciting

dd47b33

DanielYang59 commented Aug 29, 2024

View reviewed changes

DanielYang59 added 4 commits August 29, 2024 10:06

revert replacement for structureNL metadata

6d15cfd

fix from pytest import raises or mark

e7723d9

directly access MonkeyPatch when pytest is already imported

0fa24b8

Merge branch 'master' into http-to-https

c7aa6df

DanielYang59 mentioned this pull request Aug 30, 2024

Fix PT013: incorrect import of pytest #4022

Closed

DanielYang59 changed the title ~~Replace HTTP URLs with HTTPS~~ Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark Aug 30, 2024

DanielYang59 requested a review from janosh August 30, 2024 03:49

janosh added docs Documentation, examples, user guides security Security issues or fixes labels Aug 30, 2024

janosh approved these changes Aug 30, 2024

View reviewed changes

regenerate documents

ddc7062

janosh merged commit 934013b into materialsproject:master Aug 30, 2024
42 checks passed

DanielYang59 deleted the http-to-https branch August 30, 2024 06:03

DanielYang59 mentioned this pull request Aug 30, 2024

[Dev/CI] Check for accessibility of hyperlinks in CI #4024

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Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` #4021

Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` #4021

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janosh commented Aug 30, 2024

DanielYang59 commented Aug 30, 2024

	for hist in self.history:
	snl_metadata = hist.pop("_snl", {})
	history += [
	{
	"name": snl_metadata.pop("name", "pymatgen"),
	"url": snl_metadata.pop("url", "http://pypi.python.org/pypi/pymatgen"),
	"description": hist,
	}
	]

Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark #4021

Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark #4021

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Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` #4021

Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` #4021

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