Packaging improvements #92

corentinravoux · 2025-12-03T13:13:44Z

A lot of change to improve the readability of flip. For now it includes:

Linting error fix with Ruff
Docstring generation
Implementation of an help mode for each submodules

Planned change in this PR:

Package reformating: Implementation of different field level methods
Description of covariance models & testing the necessary input parameters
Improve the online documentation
Improve the tests and make the workflow in github

Copilot

Pull request overview

This pull request focuses on improving the code quality and documentation of the flip package through linting fixes, comprehensive docstring generation, and structural improvements.

Key Changes

Replaced bare except: with specific except ImportError: for better error handling
Renamed config.py to _config.py and updated all imports accordingly
Added comprehensive Google-style docstrings across all modules
Improved variable naming (e.g., l → ell for mathematical clarity)
Replaced eval() calls with safer importlib and getattr() patterns
Fixed type comparisons from type(x) == type(None) to x is not None

Reviewed changes

Copilot reviewed 34 out of 35 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
flip/utils.py	Added docstrings for utility functions
flip/likelihood.py	Import path fix + comprehensive class/method documentation
flip/power_spectra/*.py	Exception handling improvements + docstrings
flip/covariance/*.py	Import path updates, variable renaming (`l`→`ell`), docstrings
flip/fitter.py	Reorganized imports + added docstrings
flip/data_vector/*.py	Import path updates + docstrings
flip/_config.py	New configuration file (renamed from `config.py`)

Comments suppressed due to low confidence (2)

flip/covariance/lai22/symbolic.py:143

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    f = open(filename, "w")

flip/covariance/symbolic.py:201

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    f = open(filename, "w")

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Copilot · 2025-12-03T13:16:27Z

flip/power_spectra/generator.py

+    model_function = importlib.import_module(
+        f"flip.power_spectra.models.get_{power_spectrum_model}_model"
+    )


Incorrect usage of importlib.import_module. This function imports a module, not a function. The code should be:

models = importlib.import_module(f"flip.power_spectra.models") model_function = getattr(models, f"get_{power_spectrum_model}_model")

The current code will fail at runtime with an ImportError since flip.power_spectra.models.get_{power_spectrum_model}_model is not a module path.

Copilot · 2025-12-03T13:16:27Z

flip/covariance/analytical/adamsblake17plane/generator.py

@@ -147,6 +236,7 @@ def covariance_gg(
    size_batch=100_000,
    number_worker=8,
 ):
+    """Compute density-density covariance (plane-parallel)."


Missing closing quote in docstring. The line should end with:

"""Compute density-density covariance (plane-parallel)."""

Suggested change

"""Compute density-density covariance (plane-parallel)."

"""Compute density-density covariance (plane-parallel)."""

Copilot · 2025-12-03T13:16:28Z

flip/covariance/fitter.py

+        """Create an emcee sampler with optional HDF backend.

+        Args:
+            likelihood (Callable): Log-probability function.
+            p0 (numpy.ndarray, optional): Initial positions.
+            backend_file (str, optional): HDF backend filename to resume/checkpoint.
+        """


Misplaced docstring. The docstring should be inside the __init__ method, not after the super().__init__() call. Move lines 481-487 to be the first line after the function signature on line 479.

Copilot · 2025-12-03T13:16:28Z

flip/covariance/generator.py

+        """Evaluate and optionally regularize M(k) term.
+
+        Applies one of the supported regularizations to stabilize numerical
+        behavior (mpmath high-precision, Savitzky–Golay smoothing, or low-k
+        asymptote detection).
+
+        Args:
+            M_function (callable): Function returning M(k) given additional parameters.
+            wavenumber (ndarray): k samples.
+            regularize_M_terms (dict|None): Per type regularization option.
+            covariance_type (str): `"gg"`, `"gv"`, or `"vv"`.
+            flip_terms (module): Terms module to switch backend when needed.
+            additional_parameters_values (dict|tuple): Extra parameters for M.
+            savgol_window (int): Window size for Savitzky–Golay.
+            savgol_polynomial (int): Polynomial order for Savitzky–Golay.
+            lowk_unstable_threshold (float): Threshold for low-k asymptote detection.
+            lowk_unstable_mean_filtering (int): Window for mean filtering indices.
+            mpmmath_decimal_precision (int): Decimal precision for mpmath.
+
+        Returns:
+            ndarray: Evaluated M(k) after regularization.
+        """


Misplaced docstring inside function body. The docstring for regularize_M should start on line 239, not line 240. Move the entire docstring block (lines 240-261) to immediately after line 239.

Suggested change

"""Evaluate and optionally regularize M(k) term.

Applies one of the supported regularizations to stabilize numerical

behavior (mpmath high-precision, Savitzky–Golay smoothing, or low-k

asymptote detection).

Args:

M_function (callable): Function returning M(k) given additional parameters.

wavenumber (ndarray): k samples.

regularize_M_terms (dict|None): Per type regularization option.

covariance_type (str): `"gg"`, `"gv"`, or `"vv"`.

flip_terms (module): Terms module to switch backend when needed.

additional_parameters_values (dict|tuple): Extra parameters for M.

savgol_window (int): Window size for Savitzky–Golay.

savgol_polynomial (int): Polynomial order for Savitzky–Golay.

lowk_unstable_threshold (float): Threshold for low-k asymptote detection.

lowk_unstable_mean_filtering (int): Window for mean filtering indices.

mpmmath_decimal_precision (int): Decimal precision for mpmath.

Returns:

ndarray: Evaluated M(k) after regularization.

"""

"""Evaluate and optionally regularize M(k) term.

Applies one of the supported regularizations to stabilize numerical

behavior (mpmath high-precision, Savitzky–Golay smoothing, or low-k

asymptote detection).

Args:

M_function (callable): Function returning M(k) given additional parameters.

wavenumber (ndarray): k samples.

regularize_M_terms (dict|None): Per type regularization option.

covariance_type (str): `"gg"`, `"gv"`, or `"vv"`.

flip_terms (module): Terms module to switch backend when needed.

additional_parameters_values (dict|tuple): Extra parameters for M.

savgol_window (int): Window size for Savitzky–Golay.

savgol_polynomial (int): Polynomial order for Savitzky–Golay.

lowk_unstable_threshold (float): Threshold for low-k asymptote detection.

lowk_unstable_mean_filtering (int): Window for mean filtering indices.

mpmmath_decimal_precision (int): Decimal precision for mpmath.

Returns:

ndarray: Evaluated M(k) after regularization.

"""

Copilot · 2025-12-03T13:16:28Z

flip/covariance/fitter.py

@@ -331,7 +299,7 @@ def run(self, migrad=True, hesse=False, minos=False, n_iter=1):
        if minos:
            try:
                log.add(self.minuit.minos())
-            except:
+            except RuntimeError:


'except' clause does nothing but pass and there is no explanatory comment.

Suggested change

except RuntimeError:

except RuntimeError:

# minuit.minos() may fail for some parameter configurations; ignore and proceed.

corentinravoux · 2025-12-11T16:28:16Z

Rather simple tests are working now

…ld, still small sample, need to rerun the notebooks and tests

corentinravoux · 2025-12-19T13:24:34Z

Tests improved and test pipeline working. Adding a script to refresh the test values

…les: forward modeling, sbi

corentinravoux · 2025-12-19T15:47:07Z

Fisher seems broken (blocked) with JAX at the moment

…is only for the covariance method

corentinravoux · 2026-01-23T14:03:15Z

New changes:

Package reformating: Possibility to create a framework for SBI or forward modeling

Improve the tests and make the workflow in github

Changes for future PR:

Description of covariance models & testing the necessary input parameters

```
Improve the online documentation
```

corentinravoux · 2026-01-23T14:07:21Z

According to the extension of package,

Data Vector specific for Fisher were removed
The computation of covariance directly from data vectors is still possible, but not the default

Copilot

Pull request overview

Copilot reviewed 76 out of 119 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (3)

flip/covariance/fitter.py:304

'except' clause does nothing but pass and there is no explanatory comment.
flip/covariance/analytical/lai22/symbolic.py:143
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flip/covariance/symbolic.py:201
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Copilot · 2026-01-23T14:11:27Z

flip/data/load_data_test.py

+    from flip import utils
+
+    (kmm, pmm), (kmt, pmt), (ktt, ptt) = load_power_spectra()
+    power_spectrum_dict = {


This assignment to 'power_spectrum_dict' is unnecessary as it is redefined before this value is used.

Copilot · 2026-01-23T14:11:27Z

flip/data_vector/basic.py

        return self._data

    @abc.abstractmethod
    def give_data_and_variance(self, **kwargs):


Overridden method signature does not match call, where it is passed too many arguments. Overriding method method Dens.give_data_and_variance matches the call.
Overridden method signature does not match call, where it is passed too many arguments. Overriding method method DirectVel.give_data_and_variance matches the call.
Overridden method signature does not match call, where it is passed too many arguments. Overriding method method DirectVel.give_data_and_variance matches the call.
Overridden method signature does not match call, where it is passed too many arguments. Overriding method method Dens.give_data_and_variance matches the call.
Overridden method signature does not match call, where it is passed too many arguments. Overriding method method DirectVel.give_data_and_variance matches the call.
Overridden method signature does not match call, where it is passed too many arguments. Overriding method method DensVel.give_data_and_variance matches the call.

corentinravoux · 2026-01-23T14:17:25Z

This branch is major and will be the basis for v1.2 once the versioning pipeline works

Copilot

Pull request overview

Copilot reviewed 76 out of 119 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (3)

flip/covariance/fitter.py:304

'except' clause does nothing but pass and there is no explanatory comment.
flip/covariance/analytical/lai22/symbolic.py:143
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flip/covariance/symbolic.py:201
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corentinravoux added 3 commits December 3, 2025 10:25

kick fix of emulatiors

69de2c1

Fixing all ruff linting warning except __init__

9f0a9dd

Regeneration of all docstring from copilot with google format

d2ed309

Copilot AI review requested due to automatic review settings December 3, 2025 13:13

Copilot started reviewing on behalf of corentinravoux December 3, 2025 13:14 View session

Copilot finished reviewing on behalf of corentinravoux December 3, 2025 13:14

Copilot AI reviewed Dec 3, 2025

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corentinravoux added 6 commits December 3, 2025 15:23

action correction test

e55c754

fix

403fd89

correct one messy pydoc

7a735af

installing cosmoprimo for the tests

68b7392

Correcting a bug introduced by BASTIEEEEEEENNNN :p

6421db8

fixing bugs

70dc396

corentinravoux added 3 commits December 18, 2025 16:44

changing flip data to include more realistic velocity and density fie…

c7668cd

…ld, still small sample, need to rerun the notebooks and tests

recreate all the test

08d7201

fix tests

f8abc4f

corentinravoux added 3 commits December 19, 2025 14:54

Reorganization of the package to start the inclusion of other submodu…

e705e7b

…les: forward modeling, sbi

fix

cf6e545

correcting all the scripts and fix bugs introduced

30ca043

corentinravoux added 8 commits December 19, 2025 16:49

fix install in tests

b11f12a

test removing conftest

2966259

moving of all the models into analytical, cleaner structure

8bc866f

correcting the main notebooks

f6fac2e

moving secret logo call

a453e1e

fix

af4f0f3

fix tests

54f1798

retiring Fisher vectors, as the regular vectors work, and the Fisher …

b3bfa66

…is only for the covariance method

corentinravoux added 5 commits January 19, 2026 17:54

beginning of fisher debugging, rcrk24 seems bugged right now, to check

dc065a4

small fix for fisher and zdep models

26ec6a8

fix all notebooks

9b83996

fix one notebook

6e94637

fix bug

7d2c31d

corentinravoux linked an issue Jan 23, 2026 that may be closed by this pull request

Expand to include forward modeling methods #87

Closed

corentinravoux requested review from bastiencarreres and Copilot January 23, 2026 14:08

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copilot reviews

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revert shitty AI comments

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corentinravoux requested a review from Copilot January 23, 2026 14:26

Copilot started reviewing on behalf of corentinravoux January 23, 2026 14:26 View session

corentinravoux merged commit 2b140ef into main Jan 23, 2026
7 checks passed

corentinravoux deleted the packaging_improvements branch January 23, 2026 14:28

Copilot AI reviewed Jan 23, 2026

View reviewed changes

	"""Compute density-density covariance (plane-parallel)."
	"""Compute density-density covariance (plane-parallel)."""

	except RuntimeError:
	except RuntimeError:
	# minuit.minos() may fail for some parameter configurations; ignore and proceed.

Packaging improvements #92

Packaging improvements #92

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corentinravoux commented Jan 23, 2026 •

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