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Simplify file structure #51

Merged
merged 6 commits into from
Jul 24, 2023
Merged

Simplify file structure #51

merged 6 commits into from
Jul 24, 2023

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dachengx
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Change the package version to 0.0.0.

Separate used and unwed functions in original utils.py to utils.py and _utils.py.

The inherited unused files and folders are named _*.

github-actions[bot]
github-actions bot reviewed Jul 21, 2023
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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

pep8

alea/_utils.py|74 col 19| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|76 col 55| W504 line break after binary operator
alea/_utils.py|78 col 17| N400: Found backslash that is used for line breaking
alea/_utils.py|79 col 101| E501 line too long (104 > 100 characters)
alea/_utils.py|81 col 35| W504 line break after binary operator
alea/_utils.py|90 col 1| D200 One-line docstring should fit on one line with quotes
alea/_utils.py|90 col 1| D208 Docstring is over-indented
alea/_utils.py|106 col 55| W504 line break after binary operator
alea/_utils.py|114 col 13| N400: Found backslash that is used for line breaking
alea/_utils.py|116 col 42| W504 line break after binary operator
alea/_utils.py|120 col 19| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|122 col 55| W504 line break after binary operator
alea/_utils.py|124 col 17| N400: Found backslash that is used for line breaking
alea/_utils.py|125 col 101| E501 line too long (104 > 100 characters)
alea/_utils.py|127 col 35| W504 line break after binary operator
alea/_utils.py|133 col 1| D103 Missing docstring in public function
alea/_utils.py|136 col 1| S603 subprocess call - check for execution of untrusted input.
alea/_utils.py|138 col 33| WPS342 Found implicit raw string: "\n"
alea/_utils.py|139 col 5| B001 Do not use bare except:, it also catches unexpected events like memory errors, interrupts, system exit, and so on. Prefer except Exception:. If you're sure what you're doing, be explicit and write except BaseException:.
alea/_utils.py|139 col 5| E722 do not use bare 'except'
alea/_utils.py|144 col 17| B006 Do not use mutable data structures for argument defaults. They are created during function definition time. All calls to the function reuse this one instance of that data structure, persisting changes between them.
alea/_utils.py|144 col 17| WPS404 Found complex default value
alea/_utils.py|145 col 27| E262 inline comment should start with '# '
alea/_utils.py|147 col 22| E262 inline comment should start with '# '
alea/_utils.py|148 col 18| WPS404 Found complex default value
alea/_utils.py|148 col 29| E262 inline comment should start with '# '
alea/_utils.py|149 col 101| E501 line too long (110 > 100 characters)
alea/_utils.py|151 col 5| E129 visually indented line with same indent as next logical line
alea/_utils.py|152 col 1| D208 Docstring is over-indented
alea/_utils.py|153 col 101| E501 line too long (119 > 100 characters)
alea/_utils.py|179 col 17| WPS348 Found a line that starts with a dot
alea/_utils.py|185 col 1| S603 subprocess call - check for execution of untrusted input.
alea/_utils.py|189 col 1| D103 Missing docstring in public function
alea/_utils.py|203 col 1| D103 Missing docstring in public function
alea/_utils.py|217 col 1| D103 Missing docstring in public function
alea/_utils.py|220 col 101| E501 line too long (133 > 100 characters)
alea/_utils.py|222 col 101| E501 line too long (121 > 100 characters)
alea/_utils.py|224 col 13| WPS529 Found implicit .get() dict usage
alea/_utils.py|242 col 9| WPS528 Found implicit .items() usage
alea/_utils.py|267 col 1| WPS338 Found incorrect order of methods in a class
alea/_utils.py|267 col 1| WPS230 Found too many public instance attributes: 15 > 6
alea/_utils.py|267 col 1| WPS214 Found too many methods: 8 > 7
alea/_utils.py|268 col 1| D204 1 blank line required after class docstring
alea/_utils.py|268 col 1| D209 Multi-line docstring closing quotes should be on a separate line
alea/_utils.py|271 col 1| D107 Missing docstring in init
alea/_utils.py|295 col 1| D102 Missing docstring in public method
alea/_utils.py|304 col 1| D102 Missing docstring in public method
alea/_utils.py|311 col 13| WPS500 Found else in a loop without break
alea/_utils.py|322 col 13| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|326 col 13| WPS352 Found multiline loop
alea/_utils.py|340 col 9| F841 local variable 'l_dict_to_append' is assigned to but never used
alea/_utils.py|342 col 13| F841 local variable 'dict_to_append' is assigned to but never used
alea/_utils.py|342 col 30| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|343 col 13| WPS352 Found multiline loop
alea/_utils.py|343 col 17| B007 Loop control variable 'idx' not used within the loop body. If this is intended, start the name with an underscore.
alea/_utils.py|347 col 1| E800 Found commented out code
alea/_utils.py|349 col 1| E800 Found commented out code
alea/_utils.py|351 col 27| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|364 col 1| D102 Missing docstring in public method
alea/_utils.py|374 col 1| D402 First line should not be the function's "signature"
alea/_utils.py|381 col 5| WPS221 Found line with high Jones Complexity: 16 > 14
alea/_utils.py|403 col 1| S101 Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
alea/_utils.py|403 col 5| WPS221 Found line with high Jones Complexity: 20 > 14
alea/_utils.py|403 col 12| WPS222 Found a condition with too much logic: 5 > 4
alea/_utils.py|403 col 101| E501 line too long (185 > 100 characters)
alea/_utils.py|412 col 65| C812 missing trailing comma
alea/_utils.py|415 col 8| WPS507 Found useless len() compare
alea/_utils.py|417 col 13| WPS221 Found line with high Jones Complexity: 15 > 14
alea/_utils.py|432 col 16| WPS507 Found useless len() compare
alea/_utils.py|435 col 101| E501 line too long (119 > 100 characters)
alea/_utils.py|435 col 120| C813 missing trailing comma in Python 3
alea/_utils.py|442 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|445 col 5| WPS500 Found else in a loop without break
alea/_utils.py|453 col 1| D103 Missing docstring in public function
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 7
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 4
alea/_utils.py|458 col 17| WPS337 Found multiline conditions
alea/_utils.py|460 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|461 col 94| C812 missing trailing comma
alea/_utils.py|463 col 101| E501 line too long (103 > 100 characters)
alea/_utils.py|472 col 25| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|472 col 25| WPS220 Found too deep nesting: 24 > 20
alea/_utils.py|473 col 98| C812 missing trailing comma
alea/_utils.py|478 col 17| WPS337 Found multiline conditions
alea/_utils.py|481 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|482 col 94| C812 missing trailing comma
alea/_utils.py|489 col 1| D103 Missing docstring in public function
alea/_utils.py|493 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|494 col 90| C812 missing trailing comma
alea/_utils.py|496 col 101| E501 line too long (109 > 100 characters)
alea/_utils.py|499 col 17| WPS529 Found implicit .get() dict usage
alea/_utils.py|504 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|505 col 94| C812 missing trailing comma
alea/_utils.py|511 col 1| D103 Missing docstring in public function
alea/_utils.py|513 col 23| WPS204 Found overused expression: parameters_to_vary[k]; used 5 > 4
alea/_utils.py|515 col 37| C416 Unnecessary list comprehension - rewrite using list().
alea/_utils.py|528 col 35| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|534 col 8| WPS507 Found useless len() compare
alea/_utils.py|540 col 1| D103 Missing docstring in public function
alea/_utils.py|540 col 1| WPS238 Found too many raises in a function: 4 > 3
alea/_utils.py|549 col 13| F841 local variable 'l_dicts' is assigned to but never used
alea/_utils.py|551 col 17| WPS221 Found line with high Jones Complexity: 19 > 14
alea/_utils.py|555 col 46| C812 missing trailing comma
alea/_utils.py|562 col 25| W503 line break before binary operator
alea/_utils.py|568 col 77| W504 line break after binary operator
alea/_utils.py|572 col 8| WPS507 Found useless len() compare
alea/_utils.py|575 col 42| E741 ambiguous variable name 'l'
alea/_utils.py|580 col 21| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|580 col 22| WPS441 Found control variable used after block: key
alea/_utils.py|580 col 27| WPS441 Found control variable used after block: value
alea/_utils.py|583 col 8| WPS507 Found useless len() compare
alea/_utils.py|585 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|586 col 85| C812 missing trailing comma
alea/_utils.py|589 col 9| WPS513 Found implicit elif condition
alea/_utils.py|591 col 88| C813 missing trailing comma in Python 3
alea/_utils.py|594 col 8| WPS507 Found useless len() compare
alea/_utils.py|600 col 1| D103 Missing docstring in public function
alea/_utils.py|600 col 1| WPS213 Found too many expressions: 18 > 9
alea/_utils.py|608 col 68| C812 missing trailing comma
alea/_utils.py|611 col 5| WPS500 Found else in a loop without break
alea/_utils.py|619 col 12| WPS507 Found useless len() compare
alea/_utils.py|620 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|626 col 9| WPS500 Found else in a loop without break
alea/_utils.py|627 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|632 col 14| N806 variable 'modified_RG_and_RGX' in function should be lowercase
alea/_utils.py|645 col 21| WPS204 Found overused expression: data[data_mask]; used 6 > 4
alea/_utils.py|710 col 1| D103 Missing docstring in public function
alea/_utils.py|712 col 1| S301 Pickle and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue.
alea/_utils.py|720 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|722 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|740 col 101| E501 line too long (102 > 100 characters)
alea/_utils.py|748 col 101| E501 line too long (103 > 100 characters)
alea/template_source.py|15 col 1| D204 1 blank line required after class docstring
alea/template_source.py|19 col 101| E501 line too long (102 > 100 characters)
alea/template_source.py|159 col 1| E800 Found commented out code
alea/template_source.py|203 col 9| WPS352 Found multiline loop
alea/template_source.py|222 col 25| WPS220 Found too deep nesting: 24 > 20
alea/template_source.py|258 col 1| E800 Found commented out code
alea/template_source.py|259 col 1| E800 Found commented out code
alea/template_source.py|261 col 1| E800 Found commented out code
alea/template_source.py|262 col 1| E800 Found commented out code
alea/template_source.py|263 col 1| E800 Found commented out code
alea/template_source.py|264 col 1| E800 Found commented out code
alea/template_source.py|265 col 1| E800 Found commented out code
alea/template_source.py|266 col 1| E800 Found commented out code
alea/template_source.py|310 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|310 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|321 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|321 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|374 col 1| RST206 Field list ends without a blank line; unexpected unindent.
alea/template_source.py|402 col 9| WPS221 Found line with high Jones Complexity: 16 > 14
alea/template_source.py|497 col 1| E800 Found commented out code
alea/utils.py|8 col 1| D103 Missing docstring in public function
alea/utils.py|14 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/utils.py|66 col 13| WPS441 Found control variable used after block: template_folder
alea/simulators.py|6 col 1| WPS301 Found dotted raw import: scipy.stats
alea/_likelihoods/ll_nt_from_config.py|11 col 1| WPS436 Found protected module import: _plotting
alea/models/init.py|1 col 1| D104 Missing docstring in public package
alea/models/init.py|2 col 1| WPS458 Found imports collision: gaussian_model

@dachengx dachengx marked this pull request as ready for review July 21, 2023 19:41
github-actions[bot]
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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

pep8

alea/_utils.py|179 col 17| WPS348 Found a line that starts with a dot
alea/_utils.py|185 col 1| S603 subprocess call - check for execution of untrusted input.
alea/_utils.py|189 col 1| D103 Missing docstring in public function
alea/_utils.py|203 col 1| D103 Missing docstring in public function
alea/_utils.py|217 col 1| D103 Missing docstring in public function
alea/_utils.py|220 col 101| E501 line too long (133 > 100 characters)
alea/_utils.py|222 col 101| E501 line too long (121 > 100 characters)
alea/_utils.py|224 col 13| WPS529 Found implicit .get() dict usage
alea/_utils.py|242 col 9| WPS528 Found implicit .items() usage
alea/_utils.py|267 col 1| WPS338 Found incorrect order of methods in a class
alea/_utils.py|267 col 1| WPS230 Found too many public instance attributes: 15 > 6
alea/_utils.py|267 col 1| WPS214 Found too many methods: 8 > 7
alea/_utils.py|268 col 1| D204 1 blank line required after class docstring
alea/_utils.py|268 col 1| D209 Multi-line docstring closing quotes should be on a separate line
alea/_utils.py|271 col 1| D107 Missing docstring in init
alea/_utils.py|295 col 1| D102 Missing docstring in public method
alea/_utils.py|304 col 1| D102 Missing docstring in public method
alea/_utils.py|311 col 13| WPS500 Found else in a loop without break
alea/_utils.py|322 col 13| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|326 col 13| WPS352 Found multiline loop
alea/_utils.py|340 col 9| F841 local variable 'l_dict_to_append' is assigned to but never used
alea/_utils.py|342 col 13| F841 local variable 'dict_to_append' is assigned to but never used
alea/_utils.py|342 col 30| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|343 col 13| WPS352 Found multiline loop
alea/_utils.py|343 col 17| B007 Loop control variable 'idx' not used within the loop body. If this is intended, start the name with an underscore.
alea/_utils.py|347 col 1| E800 Found commented out code
alea/_utils.py|349 col 1| E800 Found commented out code
alea/_utils.py|351 col 27| C408 Unnecessary dict call - rewrite as a literal.
alea/_utils.py|364 col 1| D102 Missing docstring in public method
alea/_utils.py|374 col 1| D402 First line should not be the function's "signature"
alea/_utils.py|381 col 5| WPS221 Found line with high Jones Complexity: 16 > 14
alea/_utils.py|403 col 1| S101 Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
alea/_utils.py|403 col 5| WPS221 Found line with high Jones Complexity: 20 > 14
alea/_utils.py|403 col 12| WPS222 Found a condition with too much logic: 5 > 4
alea/_utils.py|403 col 101| E501 line too long (185 > 100 characters)
alea/_utils.py|412 col 65| C812 missing trailing comma
alea/_utils.py|415 col 8| WPS507 Found useless len() compare
alea/_utils.py|417 col 13| WPS221 Found line with high Jones Complexity: 15 > 14
alea/_utils.py|432 col 16| WPS507 Found useless len() compare
alea/_utils.py|435 col 101| E501 line too long (119 > 100 characters)
alea/_utils.py|435 col 120| C813 missing trailing comma in Python 3
alea/_utils.py|442 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|445 col 5| WPS500 Found else in a loop without break
alea/_utils.py|453 col 1| D103 Missing docstring in public function
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 7
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 4
alea/_utils.py|458 col 17| WPS337 Found multiline conditions
alea/_utils.py|460 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|461 col 94| C812 missing trailing comma
alea/_utils.py|463 col 101| E501 line too long (103 > 100 characters)
alea/_utils.py|472 col 25| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|472 col 25| WPS220 Found too deep nesting: 24 > 20
alea/_utils.py|473 col 98| C812 missing trailing comma
alea/_utils.py|478 col 17| WPS337 Found multiline conditions
alea/_utils.py|481 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|482 col 94| C812 missing trailing comma
alea/_utils.py|489 col 1| D103 Missing docstring in public function
alea/_utils.py|493 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|494 col 90| C812 missing trailing comma
alea/_utils.py|496 col 101| E501 line too long (109 > 100 characters)
alea/_utils.py|499 col 17| WPS529 Found implicit .get() dict usage
alea/_utils.py|504 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|505 col 94| C812 missing trailing comma
alea/_utils.py|511 col 1| D103 Missing docstring in public function
alea/_utils.py|513 col 23| WPS204 Found overused expression: parameters_to_vary[k]; used 5 > 4
alea/_utils.py|515 col 37| C416 Unnecessary list comprehension - rewrite using list().
alea/_utils.py|528 col 35| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|534 col 8| WPS507 Found useless len() compare
alea/_utils.py|540 col 1| D103 Missing docstring in public function
alea/_utils.py|540 col 1| WPS238 Found too many raises in a function: 4 > 3
alea/_utils.py|549 col 13| F841 local variable 'l_dicts' is assigned to but never used
alea/_utils.py|551 col 17| WPS221 Found line with high Jones Complexity: 19 > 14
alea/_utils.py|555 col 46| C812 missing trailing comma
alea/_utils.py|562 col 25| W503 line break before binary operator
alea/_utils.py|568 col 77| W504 line break after binary operator
alea/_utils.py|572 col 8| WPS507 Found useless len() compare
alea/_utils.py|575 col 42| E741 ambiguous variable name 'l'
alea/_utils.py|580 col 21| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|580 col 22| WPS441 Found control variable used after block: key
alea/_utils.py|580 col 27| WPS441 Found control variable used after block: value
alea/_utils.py|583 col 8| WPS507 Found useless len() compare
alea/_utils.py|585 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|586 col 85| C812 missing trailing comma
alea/_utils.py|589 col 9| WPS513 Found implicit elif condition
alea/_utils.py|591 col 88| C813 missing trailing comma in Python 3
alea/_utils.py|594 col 8| WPS507 Found useless len() compare
alea/_utils.py|600 col 1| D103 Missing docstring in public function
alea/_utils.py|600 col 1| WPS213 Found too many expressions: 18 > 9
alea/_utils.py|608 col 68| C812 missing trailing comma
alea/_utils.py|611 col 5| WPS500 Found else in a loop without break
alea/_utils.py|619 col 12| WPS507 Found useless len() compare
alea/_utils.py|620 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|626 col 9| WPS500 Found else in a loop without break
alea/_utils.py|627 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|632 col 14| N806 variable 'modified_RG_and_RGX' in function should be lowercase
alea/_utils.py|645 col 21| WPS204 Found overused expression: data[data_mask]; used 6 > 4
alea/_utils.py|710 col 1| D103 Missing docstring in public function
alea/_utils.py|712 col 1| S301 Pickle and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue.
alea/_utils.py|720 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|722 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|740 col 101| E501 line too long (102 > 100 characters)
alea/_utils.py|748 col 101| E501 line too long (103 > 100 characters)
alea/template_source.py|15 col 1| D204 1 blank line required after class docstring
alea/template_source.py|19 col 101| E501 line too long (102 > 100 characters)
alea/template_source.py|159 col 1| E800 Found commented out code
alea/template_source.py|203 col 9| WPS352 Found multiline loop
alea/template_source.py|222 col 25| WPS220 Found too deep nesting: 24 > 20
alea/template_source.py|258 col 1| E800 Found commented out code
alea/template_source.py|259 col 1| E800 Found commented out code
alea/template_source.py|261 col 1| E800 Found commented out code
alea/template_source.py|262 col 1| E800 Found commented out code
alea/template_source.py|263 col 1| E800 Found commented out code
alea/template_source.py|264 col 1| E800 Found commented out code
alea/template_source.py|265 col 1| E800 Found commented out code
alea/template_source.py|266 col 1| E800 Found commented out code
alea/template_source.py|310 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|310 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|321 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|321 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|374 col 1| RST206 Field list ends without a blank line; unexpected unindent.
alea/template_source.py|402 col 9| WPS221 Found line with high Jones Complexity: 16 > 14
alea/template_source.py|497 col 1| E800 Found commented out code
alea/utils.py|8 col 1| D103 Missing docstring in public function
alea/utils.py|14 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/utils.py|66 col 13| WPS441 Found control variable used after block: template_folder
alea/simulators.py|6 col 1| WPS301 Found dotted raw import: scipy.stats
alea/_likelihoods/ll_nt_from_config.py|11 col 1| WPS436 Found protected module import: _plotting
alea/models/init.py|1 col 1| D104 Missing docstring in public package
alea/models/init.py|2 col 1| WPS458 Found imports collision: gaussian_model

@dachengx dachengx requested review from hammannr and kdund July 21, 2023 20:40
@kdund
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kdund commented Jul 21, 2023

I guess the idea is to have this be the first step towards clearing out now-deprecated binference code, right? So first into a _folder, and then later when replaced, we delete it?

@dachengx
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I guess the idea is to have this be the first step towards clearing out now-deprecated binference code, right? So first into a _folder, and then later when replaced, we delete it?

Yes, exactly.

@dachengx
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And also do not use nested folders inside alea/alea.

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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

pep8

alea/_utils.py|381 col 5| WPS221 Found line with high Jones Complexity: 16 > 14
alea/_utils.py|403 col 1| S101 Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
alea/_utils.py|403 col 5| WPS221 Found line with high Jones Complexity: 20 > 14
alea/_utils.py|403 col 12| WPS222 Found a condition with too much logic: 5 > 4
alea/_utils.py|403 col 101| E501 line too long (185 > 100 characters)
alea/_utils.py|412 col 65| C812 missing trailing comma
alea/_utils.py|415 col 8| WPS507 Found useless len() compare
alea/_utils.py|417 col 13| WPS221 Found line with high Jones Complexity: 15 > 14
alea/_utils.py|432 col 16| WPS507 Found useless len() compare
alea/_utils.py|435 col 101| E501 line too long (119 > 100 characters)
alea/_utils.py|435 col 120| C813 missing trailing comma in Python 3
alea/_utils.py|442 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|445 col 5| WPS500 Found else in a loop without break
alea/_utils.py|453 col 1| D103 Missing docstring in public function
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 7
alea/_utils.py|456 col 31| WPS204 Found overused expression: copy_of_merged_combinations[idx]; used 8 > 4
alea/_utils.py|458 col 17| WPS337 Found multiline conditions
alea/_utils.py|460 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|461 col 94| C812 missing trailing comma
alea/_utils.py|463 col 101| E501 line too long (103 > 100 characters)
alea/_utils.py|472 col 25| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|472 col 25| WPS220 Found too deep nesting: 24 > 20
alea/_utils.py|473 col 98| C812 missing trailing comma
alea/_utils.py|478 col 17| WPS337 Found multiline conditions
alea/_utils.py|481 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|482 col 94| C812 missing trailing comma
alea/_utils.py|489 col 1| D103 Missing docstring in public function
alea/_utils.py|493 col 17| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|494 col 90| C812 missing trailing comma
alea/_utils.py|496 col 101| E501 line too long (109 > 100 characters)
alea/_utils.py|499 col 17| WPS529 Found implicit .get() dict usage
alea/_utils.py|504 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|505 col 94| C812 missing trailing comma
alea/_utils.py|511 col 1| D103 Missing docstring in public function
alea/_utils.py|513 col 23| WPS204 Found overused expression: parameters_to_vary[k]; used 5 > 4
alea/_utils.py|515 col 37| C416 Unnecessary list comprehension - rewrite using list().
alea/_utils.py|528 col 35| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|534 col 8| WPS507 Found useless len() compare
alea/_utils.py|540 col 1| D103 Missing docstring in public function
alea/_utils.py|540 col 1| WPS238 Found too many raises in a function: 4 > 3
alea/_utils.py|549 col 13| F841 local variable 'l_dicts' is assigned to but never used
alea/_utils.py|551 col 17| WPS221 Found line with high Jones Complexity: 19 > 14
alea/_utils.py|555 col 46| C812 missing trailing comma
alea/_utils.py|562 col 25| W503 line break before binary operator
alea/_utils.py|568 col 77| W504 line break after binary operator
alea/_utils.py|572 col 8| WPS507 Found useless len() compare
alea/_utils.py|575 col 42| E741 ambiguous variable name 'l'
alea/_utils.py|580 col 21| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|580 col 22| WPS441 Found control variable used after block: key
alea/_utils.py|580 col 27| WPS441 Found control variable used after block: value
alea/_utils.py|583 col 8| WPS507 Found useless len() compare
alea/_utils.py|585 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|586 col 85| C812 missing trailing comma
alea/_utils.py|589 col 9| WPS513 Found implicit elif condition
alea/_utils.py|591 col 88| C813 missing trailing comma in Python 3
alea/_utils.py|594 col 8| WPS507 Found useless len() compare
alea/_utils.py|600 col 1| D103 Missing docstring in public function
alea/_utils.py|600 col 1| WPS213 Found too many expressions: 18 > 9
alea/_utils.py|608 col 68| C812 missing trailing comma
alea/_utils.py|611 col 5| WPS500 Found else in a loop without break
alea/_utils.py|619 col 12| WPS507 Found useless len() compare
alea/_utils.py|620 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|626 col 9| WPS500 Found else in a loop without break
alea/_utils.py|627 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|632 col 14| N806 variable 'modified_RG_and_RGX' in function should be lowercase
alea/_utils.py|645 col 21| WPS204 Found overused expression: data[data_mask]; used 6 > 4
alea/_utils.py|710 col 1| D103 Missing docstring in public function
alea/_utils.py|712 col 1| S301 Pickle and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue.
alea/_utils.py|720 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|722 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|740 col 101| E501 line too long (102 > 100 characters)
alea/_utils.py|748 col 101| E501 line too long (103 > 100 characters)
alea/template_source.py|15 col 1| D204 1 blank line required after class docstring
alea/template_source.py|19 col 101| E501 line too long (102 > 100 characters)
alea/template_source.py|159 col 1| E800 Found commented out code
alea/template_source.py|203 col 9| WPS352 Found multiline loop
alea/template_source.py|222 col 25| WPS220 Found too deep nesting: 24 > 20
alea/template_source.py|258 col 1| E800 Found commented out code
alea/template_source.py|259 col 1| E800 Found commented out code
alea/template_source.py|261 col 1| E800 Found commented out code
alea/template_source.py|262 col 1| E800 Found commented out code
alea/template_source.py|263 col 1| E800 Found commented out code
alea/template_source.py|264 col 1| E800 Found commented out code
alea/template_source.py|265 col 1| E800 Found commented out code
alea/template_source.py|266 col 1| E800 Found commented out code
alea/template_source.py|310 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|310 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|321 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|321 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|374 col 1| RST206 Field list ends without a blank line; unexpected unindent.
alea/template_source.py|402 col 9| WPS221 Found line with high Jones Complexity: 16 > 14
alea/template_source.py|497 col 1| E800 Found commented out code
alea/utils.py|8 col 1| D103 Missing docstring in public function
alea/utils.py|14 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/utils.py|66 col 13| WPS441 Found control variable used after block: template_folder
alea/simulators.py|6 col 1| WPS301 Found dotted raw import: scipy.stats
alea/_likelihoods/ll_nt_from_config.py|11 col 1| WPS436 Found protected module import: _plotting
alea/models/init.py|1 col 1| D104 Missing docstring in public package
alea/models/init.py|2 col 1| WPS458 Found imports collision: gaussian_model

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coveralls commented Jul 22, 2023 •
edited
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Pull Request Test Coverage Report for Build 5632654804

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

Details

  • 0 of 482 (0.0%) changed or added relevant lines in 9 files are covered.
  • 11 unchanged lines in 3 files lost coverage.
  • Overall coverage remained the same at 0.0%
Changes Missing Coverage Covered Lines Changed/Added Lines %
alea/_likelihoods/ll_nt_from_config.py 0 1 0.0%
alea/models/gaussian_model.py 0 1 0.0%
alea/blueice_extended_model.py 0 2 0.0%
alea/models/init.py 0 2 0.0%
alea/simulators.py 0 3 0.0%
alea/init.py 0 10 0.0%
alea/utils.py 0 13 0.0%
alea/template_source.py 0 29 0.0%
alea/_utils.py 0 421 0.0%
Files with Coverage Reduction New Missed Lines %
alea/simulators.py 1 0.0%
alea/utils.py 1 0.0%
alea/template_source.py 9 0.0%
Totals Coverage Status
Change from base Build 5632534226: 0.0%
Covered Lines: 0
Relevant Lines: 2868
💛 - Coveralls

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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

pep8

alea/_utils.py|499 col 17| WPS529 Found implicit .get() dict usage
alea/_utils.py|504 col 21| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|505 col 94| C812 missing trailing comma
alea/_utils.py|511 col 1| D103 Missing docstring in public function
alea/_utils.py|513 col 23| WPS204 Found overused expression: parameters_to_vary[k]; used 5 > 4
alea/_utils.py|515 col 37| C416 Unnecessary list comprehension - rewrite using list().
alea/_utils.py|528 col 35| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|534 col 8| WPS507 Found useless len() compare
alea/_utils.py|540 col 1| D103 Missing docstring in public function
alea/_utils.py|540 col 1| WPS238 Found too many raises in a function: 4 > 3
alea/_utils.py|549 col 13| F841 local variable 'l_dicts' is assigned to but never used
alea/_utils.py|551 col 17| WPS221 Found line with high Jones Complexity: 19 > 14
alea/_utils.py|555 col 46| C812 missing trailing comma
alea/_utils.py|562 col 25| W503 line break before binary operator
alea/_utils.py|568 col 77| W504 line break after binary operator
alea/_utils.py|572 col 8| WPS507 Found useless len() compare
alea/_utils.py|575 col 42| E741 ambiguous variable name 'l'
alea/_utils.py|580 col 21| C416 Unnecessary dict comprehension - rewrite using dict().
alea/_utils.py|580 col 22| WPS441 Found control variable used after block: key
alea/_utils.py|580 col 27| WPS441 Found control variable used after block: value
alea/_utils.py|583 col 8| WPS507 Found useless len() compare
alea/_utils.py|585 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|586 col 85| C812 missing trailing comma
alea/_utils.py|589 col 9| WPS513 Found implicit elif condition
alea/_utils.py|591 col 88| C813 missing trailing comma in Python 3
alea/_utils.py|594 col 8| WPS507 Found useless len() compare
alea/_utils.py|600 col 1| D103 Missing docstring in public function
alea/_utils.py|600 col 1| WPS213 Found too many expressions: 18 > 9
alea/_utils.py|608 col 68| C812 missing trailing comma
alea/_utils.py|611 col 5| WPS500 Found else in a loop without break
alea/_utils.py|619 col 12| WPS507 Found useless len() compare
alea/_utils.py|620 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|626 col 9| WPS500 Found else in a loop without break
alea/_utils.py|627 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|632 col 14| N806 variable 'modified_RG_and_RGX' in function should be lowercase
alea/_utils.py|645 col 21| WPS204 Found overused expression: data[data_mask]; used 6 > 4
alea/_utils.py|710 col 1| D103 Missing docstring in public function
alea/_utils.py|712 col 1| S301 Pickle and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue.
alea/_utils.py|720 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|722 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|740 col 101| E501 line too long (102 > 100 characters)
alea/_utils.py|748 col 101| E501 line too long (103 > 100 characters)
alea/template_source.py|15 col 1| D204 1 blank line required after class docstring
alea/template_source.py|19 col 101| E501 line too long (102 > 100 characters)
alea/template_source.py|159 col 1| E800 Found commented out code
alea/template_source.py|203 col 9| WPS352 Found multiline loop
alea/template_source.py|222 col 25| WPS220 Found too deep nesting: 24 > 20
alea/template_source.py|258 col 1| E800 Found commented out code
alea/template_source.py|259 col 1| E800 Found commented out code
alea/template_source.py|261 col 1| E800 Found commented out code
alea/template_source.py|262 col 1| E800 Found commented out code
alea/template_source.py|263 col 1| E800 Found commented out code
alea/template_source.py|264 col 1| E800 Found commented out code
alea/template_source.py|265 col 1| E800 Found commented out code
alea/template_source.py|266 col 1| E800 Found commented out code
alea/template_source.py|310 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|310 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|321 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|321 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|374 col 1| RST206 Field list ends without a blank line; unexpected unindent.
alea/template_source.py|402 col 9| WPS221 Found line with high Jones Complexity: 16 > 14
alea/template_source.py|497 col 1| E800 Found commented out code
alea/utils.py|8 col 1| D103 Missing docstring in public function
alea/utils.py|14 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/utils.py|66 col 13| WPS441 Found control variable used after block: template_folder
alea/simulators.py|6 col 1| WPS301 Found dotted raw import: scipy.stats
alea/_likelihoods/ll_nt_from_config.py|11 col 1| WPS436 Found protected module import: _plotting
alea/models/init.py|1 col 1| D104 Missing docstring in public package
alea/models/init.py|2 col 1| WPS458 Found imports collision: gaussian_model

github-actions[bot]
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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

pep8

alea/_utils.py|619 col 12| WPS507 Found useless len() compare
alea/_utils.py|620 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|626 col 9| WPS500 Found else in a loop without break
alea/_utils.py|627 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|628 col 25| WPS465 Found likely bitwise and boolean operation mixup
alea/_utils.py|632 col 14| N806 variable 'modified_RG_and_RGX' in function should be lowercase
alea/_utils.py|645 col 21| WPS204 Found overused expression: data[data_mask]; used 6 > 4
alea/_utils.py|710 col 1| D103 Missing docstring in public function
alea/_utils.py|712 col 1| S301 Pickle and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue.
alea/_utils.py|720 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|722 col 13| WPS454 Found wrong raise exception type: Exception
alea/_utils.py|740 col 101| E501 line too long (102 > 100 characters)
alea/_utils.py|748 col 101| E501 line too long (103 > 100 characters)
alea/template_source.py|15 col 1| D204 1 blank line required after class docstring
alea/template_source.py|19 col 101| E501 line too long (102 > 100 characters)
alea/template_source.py|159 col 1| E800 Found commented out code
alea/template_source.py|203 col 9| WPS352 Found multiline loop
alea/template_source.py|222 col 25| WPS220 Found too deep nesting: 24 > 20
alea/template_source.py|258 col 1| E800 Found commented out code
alea/template_source.py|259 col 1| E800 Found commented out code
alea/template_source.py|261 col 1| E800 Found commented out code
alea/template_source.py|262 col 1| E800 Found commented out code
alea/template_source.py|263 col 1| E800 Found commented out code
alea/template_source.py|264 col 1| E800 Found commented out code
alea/template_source.py|265 col 1| E800 Found commented out code
alea/template_source.py|266 col 1| E800 Found commented out code
alea/template_source.py|310 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|310 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|321 col 37| WPS441 Found control variable used after block: histname
alea/template_source.py|321 col 47| WPS441 Found control variable used after block: templatename
alea/template_source.py|374 col 1| RST206 Field list ends without a blank line; unexpected unindent.
alea/template_source.py|402 col 9| WPS221 Found line with high Jones Complexity: 16 > 14
alea/template_source.py|497 col 1| E800 Found commented out code
alea/utils.py|8 col 1| D103 Missing docstring in public function
alea/utils.py|14 col 1| S307 Use of possibly insecure function - consider using safer ast.literal_eval.
alea/utils.py|66 col 13| WPS441 Found control variable used after block: template_folder
alea/simulators.py|6 col 1| WPS301 Found dotted raw import: scipy.stats
alea/_likelihoods/ll_nt_from_config.py|11 col 1| WPS436 Found protected module import: _plotting
alea/models/init.py|1 col 1| D104 Missing docstring in public package
alea/models/init.py|2 col 1| WPS458 Found imports collision: gaussian_model

alea/_utils.py
elif key == "signal_rate_multiplier" and combination.get("signal_expectation", None) is not None:
continue
else:
function_args[key] = value
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[pep8] reported by reviewdog 🐶
WPS529 Found implicit .get() dict usage

alea/_utils.py
if isinstance(combination["livetime"], list):
for idx, value in enumerate(combination["livetime"]):
if "livetime_" + str(idx) in function_args:
raise Exception(
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[pep8] reported by reviewdog 🐶
WPS454 Found wrong raise exception type: Exception

alea/_utils.py
for idx, value in enumerate(combination["livetime"]):
if "livetime_" + str(idx) in function_args:
raise Exception(
"You are overwriting function_args without knowing what is going on!"
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[pep8] reported by reviewdog 🐶
C812 missing trailing comma

alea/_utils.py
return function_args


def compute_parameters_to_vary(parameters_to_vary):
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[pep8] reported by reviewdog 🐶
D103 Missing docstring in public function

alea/_utils.py

def compute_parameters_to_vary(parameters_to_vary):
for k in copy.deepcopy(parameters_to_vary):
if isinstance(parameters_to_vary[k], dict):
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[pep8] reported by reviewdog 🐶
WPS204 Found overused expression: parameters_to_vary[k]; used 5 > 4

alea/_utils.py
"Cannot check sanity of zip - better provide a list like, var: [1,2,3]"
)

if len(varied_dicts_zip) == 0:
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[pep8] reported by reviewdog 🐶
WPS507 Found useless len() compare

alea/_utils.py
return varied_dicts_zip


def manipulate_toy_data(
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[pep8] reported by reviewdog 🐶
D103 Missing docstring in public function

alea/_utils.py
return varied_dicts_zip


def manipulate_toy_data(
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[pep8] reported by reviewdog 🐶
WPS213 Found too many expressions: 18 > 9

alea/_utils.py
output_dir=None):
smearing_pars = {
'[0, 10]': np.array([19.16806452, 2.80622276, 0.20968269]),
'[10, 20]': np.array([21.54000255, 2.98114261, 0.15294833])
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[pep8] reported by reviewdog 🐶
C812 missing trailing comma

alea/_utils.py
'[10, 20]': np.array([21.54000255, 2.98114261, 0.15294833])
}
l_modified_data = []
for idx, (data, ll) in enumerate(zip(data_sets, statistical_model.lls)):
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[pep8] reported by reviewdog 🐶
WPS500 Found else in a loop without break

kdund
kdund approved these changes Jul 24, 2023
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Works for me.

@dachengx dachengx merged commit 9ddecb4 into main Jul 24, 2023
@dachengx dachengx deleted the restructure branch July 24, 2023 17:49
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@kdund kdund kdund approved these changes

@hammannr hammannr Awaiting requested review from hammannr

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@dachengx @kdund @coveralls