`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` #3757

DanielYang59 · 2024-04-13T10:38:18Z

Summary

Install pyright to CI (delayed until all chunks are finished)
Related pyright fixes
Improvement on io.lobster by @JaGeo
Format tweaks (sourcery), I should not have done this (make it hard to view difference)

Need confirmation on the following:

pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster #3757 (comment)

`pyright` is commented out until all chunks are finished, otherwise everyone's CI would fail.

There are too many (713) pyright errors to fix in a single PR, I'm planning to chop up into chunks. First chunk would fix the following modules:

Side note

Unit test of io.lobster.inputs only failed on my MacOS machine: pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster #3757 (comment)
io.lobster diff method could potentially be simplified: pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster #3757 (comment)

Summary by CodeRabbit

New Features
- Enhanced the logic for setting calculation parameters based on symmetry and time reversal considerations.
- Introduced better error handling and contextual exception messages across various modules.
- Improved file handling with UTF-8 encoding for consistent data processing.
Bug Fixes
- Fixed issues with string formatting and variable initialization that affected data parsing and output consistency.
- Corrected logical errors in conditional statements that impacted computational routines.
Refactor
- Streamlined string formatting using f-strings for better readability and performance.
- Simplified and optimized various methods and functions for enhanced maintainability and clarity.
Documentation
- Updated method descriptions and error messages to be more informative and user-friendly.
Style
- Standardized variable naming and method calls to adhere to project coding standards.
Tests
- Adjusted file encoding in test setups to ensure compatibility and correctness during testing.

- Hopefully all tests have been written in such a way that they will be skipped if the underlying required package is not found

Signed-off-by: Matthew Evans <7916000+ml-evs@users.noreply.github.com>

coderabbitai · 2024-04-13T10:38:23Z

Walkthrough

The recent updates across the pymatgen library focus on improving code quality through enhanced readability, efficiency, and robustness. Changes include variable renaming for clarity, refactoring for better logic flow, and the integration of modern Python features like the walrus operator. Additionally, stricter type checking with pyright has been introduced to ensure higher code quality.

Changes

Files	Change Summary
`.github/workflows/lint.yml`, `.pre-commit-config.yaml`, `pyproject.toml`	Integrated `pyright` for improved linting and type checking.
`pymatgen/command_line/vampire_caller.py`, `pymatgen/io/.../*.py`, `pymatgen/io/.../outputs.py`, `pymatgen/io/.../inputs.py`	Variable renaming, enhanced string formatting, and logic simplification.
`pymatgen/core/...`, `pymatgen/ext/...`	Code refactoring for efficiency and readability, including regex and error handling enhancements.
`pymatgen/symmetry/...`, `pymatgen/phonon/...`, `pymatgen/transformations/...`	Updated variable naming, added checks, and refactored logic.
`pymatgen/util/...`, `dev_scripts/...`	Improved clarity in variable names, adjusted import handling, and updated encoding settings.
`tests/...`	Updated test scripts to align with code changes and ensure robustness.

Poem

🐇💻✨
Oh, hop through the fields of code, so spry,
Where bugs once lurked, now none shall lie.
With pyright by side, we leap and bound,
In cleaner pastures, our bytes resound.
Celebrate, dear friends, with vim and cheer,
For cleaner, swifter code is here! 🎉🌟

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DanielYang59 · 2024-04-13T14:07:09Z

pymatgen/io/pwscf.py

        structure = Structure(
            Lattice(lattice),
            species,
            coords,
+            # DEBUG (@DanielYang59): need input on coords_are_cartesian


Need help on io.pwscf please @janosh (I never use pwscf): coords_are_cartesian is only defined in one of the many branches, and is unbound all elsewhere:

pymatgen/pymatgen/io/pwscf.py

Lines 240 to 355 in 37d1066

@classmethod

def from_str(cls, string: str) -> Self:

"""

Reads an PWInput object from a string.

Args:

string (str): PWInput string

Returns:

PWInput object

"""

lines = list(clean_lines(string.splitlines()))

def input_mode(line):

if line[0] == "&":

return ("sections", line[1:].lower())

if "ATOMIC_SPECIES" in line:

return ("pseudo",)

if "K_POINTS" in line:

return "kpoints", line.split()[1]

if "OCCUPATIONS" in line:

return "occupations"

if "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:

return "structure", line.split()[1]

if line == "/":

return None

return mode

sections: dict[str, dict] = {

"control": {},

"system": {},

"electrons": {},

"ions": {},

"cell": {},

}

pseudo = {}

lattice = []

species = []

coords = []

structure = None

site_properties: dict[str, list] = {"pseudo": []}

mode = None

for line in lines:

mode = input_mode(line)

if mode is None:

pass

elif mode[0] == "sections":

section = mode[1]

m = re.match(r"(\w+)$?(\d*?)$?\s*=\s*(.*)", line)

if m:

key = m.group(1).strip()

key_ = m.group(2).strip()

val = m.group(3).strip()

if key_ != "":

if sections[section].get(key) is None:

val_ = [0.0] * 20 # MAX NTYP DEFINITION

val_[int(key_) - 1] = PWInput.proc_val(key, val)

sections[section][key] = val_

site_properties[key] = []

else:

sections[section][key][int(key_) - 1] = PWInput.proc_val(key, val)

else:

sections[section][key] = PWInput.proc_val(key, val)

elif mode[0] == "pseudo":

m = re.match(r"(\w+)\s+(\d*.\d*)\s+(.*)", line)

if m:

pseudo[m.group(1).strip()] = m.group(3).strip()

elif mode[0] == "kpoints":

m = re.match(r"(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)", line)

if m:

kpoints_grid = (int(m.group(1)), int(m.group(2)), int(m.group(3)))

kpoints_shift = (int(m.group(4)), int(m.group(5)), int(m.group(6)))

else:

kpoints_mode = mode[1]

kpoints_grid = (1, 1, 1)

kpoints_shift = (0, 0, 0)

elif mode[0] == "structure":

m_l = re.match(r"(-?\d+\.?\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)", line)

m_p = re.match(r"(\w+)\s+(-?\d+\.\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)", line)

if m_l:

lattice += [

float(m_l.group(1)),

float(m_l.group(2)),

float(m_l.group(3)),

]

elif m_p:

site_properties["pseudo"].append(pseudo[m_p.group(1)])

species.append(m_p.group(1))

coords += [[float(m_p.group(2)), float(m_p.group(3)), float(m_p.group(4))]]

if mode[1] == "angstrom":

coords_are_cartesian = True

elif mode[1] == "crystal":

coords_are_cartesian = False

structure = Structure(

Lattice(lattice),

species,

coords,

coords_are_cartesian=coords_are_cartesian,

site_properties=site_properties,

)

return cls(

structure=structure,

control=sections["control"],

pseudo=pseudo,

system=sections["system"],

electrons=sections["electrons"],

ions=sections["ions"],

cell=sections["cell"],

kpoints_mode=kpoints_mode,

kpoints_grid=kpoints_grid,

kpoints_shift=kpoints_shift,

)

I currently set the default coords_are_cartesian to False (the default of Structure), but I'm not sure if it's the default for pwscf too. Would need confirmation on this.

wow, so many code branches and only one of them was actually tested?

pymatgen/tests/io/test_pwscf.py

Lines 360 to 367 in 37d1066

[8.49746961, 10.62408601, 8.49746961],

[6.373854, 6.373854, 10.62565387],

[8.49746961, 8.49746961, 10.62408601],

[10.62408601, 10.62408601, 10.62408601],

]

)

pw_in = PWInput.from_str(string)

this seems in urgent need of more tests. i think defaulting coords_are_cartesian=False seems right. i also never used this code so it's hard to know for sure. apparently no one does or this would have been reported long ago

so many code branches and only one of them was actually tested?

Yes, coords_are_cartesian is defined in only one of the many branches and is unbound all elsewhere 😓, meaning the other branches were likely never entered.

coderabbitai

Actionable comments posted: 5

pymatgen/core/periodic_table.py

pymatgen/io/vasp/outputs.py

DanielYang59 · 2024-04-15T08:32:26Z

Thanks for reviewing @janosh and great to collaborate with you on this one @JaGeo.

Sorry for hijacking this topic @ml-evs.

ml-evs · 2024-04-15T08:46:29Z

Sorry for hijacking this topic @ml-evs.

No problem, this is great work! It looks this was fairly comprehensive; I'll try reopening my PR that adds the CI runs that triggered this.

JaGeo · 2024-04-15T08:51:23Z

Sorry for hijacking this topic @ml-evs.

No problem, this is great work! It looks this was fairly comprehensive; I'll try reopening my PR that adds the CI runs that triggered this.

This is only for some modules. More work is needed

DanielYang59 · 2024-04-15T08:52:45Z

This is only for some modules. More work is needed

Yes! It's only like 1/3 of the all work needed. I would ping you once it's all ready. @ml-evs

ml-evs · 2024-04-15T09:01:38Z

This is only for some modules. More work is needed

Yes! It's only like 1/3 of the all work needed. I would ping you once it's all ready. @ml-evs

Understood, I've opened #3759 with the same changes as before (except enabling pyright), hopefully the CI is now stable enough after the uv switch that it won't go stale again so quickly.

janosh · 2024-04-15T09:04:29Z

Yes! It's only like 1/3 of the all work needed. I would ping you once it's all ready. @ml-evs

@DanielYang59 thanks a lot for donating your time to work on this! 👍

DanielYang59 · 2024-04-15T09:49:53Z

@DanielYang59 thanks a lot for donating your time to work on this! 👍

Glad I can help :)

DanielYang59 · 2024-04-15T13:02:32Z

@janosh I'm still experimenting on an issue I met with @JaGeo in #3757 (comment). I would appreciate it if you could give me some advice 😄

I just created a minimal code to recreate this issue:

from collections import UserDict

class TestClass(UserDict):

    def __init__(self, settingsdict: dict):
        super().__init__()
        self.update(settingsdict)

    def __setitem__(self, key, val):
        """Remove case sensitivity."""
        new_key = next((key_here for key_here in self if key.strip().lower() == key_here.lower()), key)

        super().__setitem__(new_key, val)

    def __getitem__(self, item):
        """Implements getitem from dict to avoid problems with cases."""
        new_item = next((key_here for key_here in self if item.strip().lower() == key_here.lower()), item)

        return super().__getitem__(new_item)


if __name__ == "__main__":
    test_dict = {"ConTent": "hello", }
    test_instance = TestClass(test_dict)

    print(f"{test_instance=}")
    print(test_instance.get("content"), test_instance["content"])

On this same machine (MacOS Sonoma 14.4.1, Apple Silicon and Python managed by miniconda3).

With Python 3.10 and 3.11, I got:

(base) yang@Yang-MacBook test % python3 -V
Python 3.10.14
(base) yang@Yang-MacBook test % python3 recreate.py 
test_instance={'ConTent': 'hello'}
hello hello

(base) yang@Yang-MacBook test % python3 -V
Python 3.11.8
(base) yang@Yang-MacBook test % python3 recreate.py 
test_instance={'ConTent': 'hello'}
hello hello

While with Python 3.12, the two methods get different results:

(base) yang@Yang-MacBook test % python3 -V               
Python 3.12.2
(base) yang@Yang-MacBook test % python3 recreate.py      
test_instance={'ConTent': 'hello'}
None hello

Is it some known issue/change from Python 3.12?

JaGeo · 2024-04-15T13:05:42Z

Ah, interesting, Python version 😅.
This is why it has not shown up on CI.

JaGeo · 2024-04-15T13:07:20Z

@DanielYang59 I think I found it: python/cpython#105524

DanielYang59 · 2024-04-15T13:09:54Z

@DanielYang59 I think I found it: python/cpython#105524

👍 So speedy. Yes looks like exactly what we're experiencing. I guess it's not intended?

The get method:

    def get(self, key, default=None):
        if key in self:
            return self[key]
        return default

Which indeed does not use __getitem__.

But at least confirmed my machine is not the "outlier" 😅

JaGeo · 2024-04-15T13:24:19Z

@DanielYang59 I think I found it: python/cpython#105524

👍 So speedy. Yes looks like exactly what we're experiencing. I guess it's not intended?

The get method:
    def get(self, key, default=None):
        if key in self:
            return self[key]
        return default
Which indeed does not use __getitem__.

But at least confirmed my machine is not the "outlier" 😅

No idea if intended.
But a solution is described there as well. Could potentially affect other parts of the code as well.

janosh · 2024-04-15T17:02:05Z

there's only 1 use of UserDict in all of pmg i think. we can try the proposed fix or try to make it work without UserDict. the docs weakly recommend to subclass dict directly instead of UserDict

JaGeo · 2024-04-15T17:05:34Z

I think we recently switched to UserDict for other issues.

DanielYang59 · 2024-04-16T02:28:04Z

there's only 1 use of UserDict in all of pmg i think. we can try the proposed fix or try to make it work without UserDict. the docs weakly recommend to subclass dict directly instead of UserDict

I would keep it in mind. I'm now secretly working on simplifying io.lobster.inputs (prefer not to push it here for now because I'm not having much time to work on this).

ml-evs and others added 8 commits February 23, 2024 10:36

Add a CI run that only tests non-optional deps (optimistically)

418f3e2

- Hopefully all tests have been written in such a way that they will be skipped if the underlying required package is not found

Install dev deps at least

b0b16a6

Try out pyright config for unbound vars only

a9cf9cd

Add pyright to CI

93e9afe

Merge branch 'master' into ml-evs/ci-with-mandatory-deps

fc09e78

Signed-off-by: Matthew Evans <7916000+ml-evs@users.noreply.github.com>

pyright fix

f63b806

pyright fix in vis.structure_vtk

20d318e

fix utils

974a8b9

DanielYang59 added 16 commits April 13, 2024 18:46

fix transformations

081db43

Merge branch 'master' into pyright

28b9380

Merge branch 'master' into pyright

fa0e173

fix symmetry.kpath

d388c23

finish fixing symmetry

895f2c1

update pyright

2d7f701

suppress pyright reportMissingModuleSource warning

a6a5714

fix phonon

2063f09

some fixes in io

4ac354f

Merge branch 'master' into pyright

a9c8c78

format tweaks of io.vasp.outputs

e3d2d54

fix unit test for symmetry.kpath

afac73e

fix io.vasp

147cb85

fix unit test for io.vasp.inputs

962e4ee

fix io.qchem

2f4c6fc

fix io.pwscf, need input

87a588b

DanielYang59 commented Apr 13, 2024

View reviewed changes

DanielYang59 added 4 commits April 13, 2024 22:11

replace match.group(i) with match[i]

c3f290b

fix missing )

8ee0655

fix typo

45b59b9

suppress reportInvalidTypeForm

eddf08f

janosh added 2 commits April 15, 2024 10:03

remove unused pyright code until ready to enable

80aa33f

rename single-letter m->match

1dffaff

JaGeo approved these changes Apr 15, 2024

View reviewed changes

coderabbitai bot reviewed Apr 15, 2024

View reviewed changes

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remove unused raw

2ce0368

janosh enabled auto-merge (squash) April 15, 2024 08:15

janosh added linting Linting and quality assurance housekeeping Moving around or cleaning up old code/files labels Apr 15, 2024

janosh merged commit 0e57abf into materialsproject:master Apr 15, 2024
22 checks passed

DanielYang59 deleted the pyright branch April 15, 2024 08:31

ml-evs mentioned this pull request Apr 15, 2024

Add a CI run that only tests non-optional deps (optimistically) #3759

Closed

This was referenced Apr 20, 2024

Collect possible issues might come with Python 3.12 #3775

Closed

pyright fixes #3777

Merged

janosh mentioned this pull request Apr 30, 2024

Officially support Python 3.12 and test in CI #3685

Merged

DanielYang59 mentioned this pull request May 31, 2024

Simplify case handling in lobster.inputs #3848

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`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` #3757

`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` #3757

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	@classmethod
	def from_str(cls, string: str) -> Self:
	"""
	Reads an PWInput object from a string.

	Args:
	string (str): PWInput string

	Returns:
	PWInput object
	"""
	lines = list(clean_lines(string.splitlines()))

	def input_mode(line):
	if line[0] == "&":
	return ("sections", line[1:].lower())
	if "ATOMIC_SPECIES" in line:
	return ("pseudo",)
	if "K_POINTS" in line:
	return "kpoints", line.split()[1]
	if "OCCUPATIONS" in line:
	return "occupations"
	if "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
	return "structure", line.split()[1]
	if line == "/":
	return None
	return mode

	sections: dict[str, dict] = {
	"control": {},
	"system": {},
	"electrons": {},
	"ions": {},
	"cell": {},
	}
	pseudo = {}
	lattice = []
	species = []
	coords = []
	structure = None
	site_properties: dict[str, list] = {"pseudo": []}
	mode = None
	for line in lines:
	mode = input_mode(line)
	if mode is None:
	pass
	elif mode[0] == "sections":
	section = mode[1]
	m = re.match(r"(\w+)\(?(\d?)\)?\s=\s(.)", line)
	if m:
	key = m.group(1).strip()
	key_ = m.group(2).strip()
	val = m.group(3).strip()
	if key_ != "":
	if sections[section].get(key) is None:
	val_ = [0.0] * 20 # MAX NTYP DEFINITION
	val_[int(key_) - 1] = PWInput.proc_val(key, val)
	sections[section][key] = val_

	site_properties[key] = []
	else:
	sections[section][key][int(key_) - 1] = PWInput.proc_val(key, val)
	else:
	sections[section][key] = PWInput.proc_val(key, val)

	elif mode[0] == "pseudo":
	m = re.match(r"(\w+)\s+(\d.\d)\s+(.*)", line)
	if m:
	pseudo[m.group(1).strip()] = m.group(3).strip()
	elif mode[0] == "kpoints":
	m = re.match(r"(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)", line)
	if m:
	kpoints_grid = (int(m.group(1)), int(m.group(2)), int(m.group(3)))
	kpoints_shift = (int(m.group(4)), int(m.group(5)), int(m.group(6)))
	else:
	kpoints_mode = mode[1]
	kpoints_grid = (1, 1, 1)
	kpoints_shift = (0, 0, 0)

	elif mode[0] == "structure":
	m_l = re.match(r"(-?\d+\.?\d)\s+(-?\d+\.?\d)\s+(-?\d+\.?\d*)", line)
	m_p = re.match(r"(\w+)\s+(-?\d+\.\d)\s+(-?\d+\.?\d)\s+(-?\d+\.?\d*)", line)
	if m_l:
	lattice += [
	float(m_l.group(1)),
	float(m_l.group(2)),
	float(m_l.group(3)),
	]
	elif m_p:
	site_properties["pseudo"].append(pseudo[m_p.group(1)])
	species.append(m_p.group(1))
	coords += [[float(m_p.group(2)), float(m_p.group(3)), float(m_p.group(4))]]

	if mode[1] == "angstrom":
	coords_are_cartesian = True
	elif mode[1] == "crystal":
	coords_are_cartesian = False
	structure = Structure(
	Lattice(lattice),
	species,
	coords,
	coords_are_cartesian=coords_are_cartesian,
	site_properties=site_properties,
	)
	return cls(
	structure=structure,
	control=sections["control"],
	pseudo=pseudo,
	system=sections["system"],
	electrons=sections["electrons"],
	ions=sections["ions"],
	cell=sections["cell"],
	kpoints_mode=kpoints_mode,
	kpoints_grid=kpoints_grid,
	kpoints_shift=kpoints_shift,
	)

	[8.49746961, 10.62408601, 8.49746961],
	[6.373854, 6.373854, 10.62565387],
	[8.49746961, 8.49746961, 10.62408601],
	[10.62408601, 10.62408601, 10.62408601],
	]
	)

	pw_in = PWInput.from_str(string)

pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster #3757

pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster #3757

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DanielYang59 commented Apr 13, 2024 • edited Loading

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pyright is commented out until all chunks are finished, otherwise everyone's CI would fail.

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`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` #3757

`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/dev_scripts` and improve `io.lobster` #3757

DanielYang59 commented Apr 13, 2024 •

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`pyright` is commented out until all chunks are finished, otherwise everyone's CI would fail.

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