Remove 'src' prefix from imports - standardize package structure by Copilot · Pull Request #17 · Pablo1990/pyVertexModel

Copilot · 2026-02-03T16:08:36Z

Project imports used non-standard from src.pyVertexModel pattern. Updated to standard from pyVertexModel convention.

Changes

Package configuration:

setup.py: Added package_dir={'': 'src'} with find_packages(where='src')
Cython extension path: src.pyVertexModel.Kg.kg_functions → pyVertexModel.Kg.kg_functions

Import updates (54 files):

from src.pyVertexModel.* → from pyVertexModel.*
from src import PROJECT_DIRECTORY, logger → from pyVertexModel import PROJECT_DIRECTORY, logger

Cleanup:

Moved PROJECT_DIRECTORY and logger from src/__init__.py to src/pyVertexModel/__init__.py
Removed obsolete src/__init__.py and redundant pyVertexModel/ root directory
Replaced nested os.path.dirname() with Path(__file__).parent.parent.parent for clarity

Usage

# Before
from src.pyVertexModel.geometry.cell import Cell
from src.pyVertexModel.algorithm.vertexModel import VertexModel
from src import PROJECT_DIRECTORY

# After
from pyVertexModel.geometry.cell import Cell
from pyVertexModel.algorithm.vertexModel import VertexModel
from pyVertexModel import PROJECT_DIRECTORY

Original prompt

This section details on the original issue you should resolve

<issue_title>Import project without 'src'</issue_title>
<issue_description>The project is currently being importer using 'src'. It should not happen.</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes Import project without 'src' #16

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

…ucture Co-authored-by: Pablo1990 <1974224+Pablo1990@users.noreply.github.com>

Co-authored-by: Pablo1990 <1974224+Pablo1990@users.noreply.github.com>

coderabbitai · 2026-02-04T10:00:20Z

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Copilot

Pull request overview

This pull request standardizes the package structure by removing the non-standard 'src' prefix from imports and adopting the standard src-layout pattern. The changes affect 54 files across the codebase.

Changes:

Updated all imports from from src.pyVertexModel.* to from pyVertexModel.* across 54 files
Configured setup.py to use src-layout with package_dir={'': 'src'} and find_packages(where='src')
Moved PROJECT_DIRECTORY and logger initialization from src/__init__.py to src/pyVertexModel/__init__.py

Reviewed changes

Copilot reviewed 59 out of 62 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
setup.py	Updated to use find_packages with src directory, changed Cython extension name
src/pyVertexModel/init.py	Added PROJECT_DIRECTORY and logger setup (moved from src/init.py)
src/init.py	Removed (functionality moved to pyVertexModel/init.py)
pyVertexModel/init.py	Removed redundant root-level package init
src/pyVertexModel/gui/qt_gui.py	Entire file deleted (174 lines)
src/pyVertexModel/algorithm/vertexModel.py	Updated imports, added local PROJECT_DIRECTORY redefinition
src/pyVertexModel/algorithm/vertexModelVoronoiFromTimeImage.py	Updated imports, added local PROJECT_DIRECTORY redefinition
src/pyVertexModel/algorithm/vertexModelBubbles.py	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/algorithm/VertexModelVoronoi3D.py	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/algorithm/newtonRaphson.py	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/Kg/*.py (8 files)	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/geometry/*.py (5 files)	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/mesh_remodelling/*.py (2 files)	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/parameters/set.py	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/util/space_exploration.py	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/analysis/*.py (11 files)	Updated imports from src.pyVertexModel to pyVertexModel
src/pyVertexModel/main*.py (4 files)	Updated imports from src.pyVertexModel to pyVertexModel
Tests/*.py (11 files)	Updated imports from src.pyVertexModel to pyVertexModel
.idea/pyVertexModel.iml	Added src as source folder, updated Python SDK reference
.github/workflows/tests.yaml	Removed 'megha' branch and pull_request trigger

Files not reviewed (1)

.idea/pyVertexModel.iml: Language not supported

Comments suppressed due to low confidence (63)

Tests/tests.py:49

assertTrue(a in b) cannot provide an informative message. Using assertIn(a, b) instead will give more informative messages.

        self.assertTrue('Geo' in mat_info)

Tests/tests.py:54

assertTrue(a in b) cannot provide an informative message. Using assertIn(a, b) instead will give more informative messages.

        self.assertTrue('Set' in mat_info)

src/pyVertexModel/analysis/analyse_pre_ablation_state.py:60

This comment appears to contain commented-out code.
src/pyVertexModel/analysis/analyse_simulation.py:405
This comment appears to contain commented-out code.
src/pyVertexModel/analysis/analyse_simulation.py:436
This comment appears to contain commented-out code.
src/pyVertexModel/analysis/analysis_megha.py:450
This comment appears to contain commented-out code.
src/pyVertexModel/geometry/cell.py:467
This comment appears to contain commented-out code.
src/pyVertexModel/analysis/find_required_purse_string.py:40
This comment appears to contain commented-out code.
src/pyVertexModel/geometry/geo.py:764
This comment appears to contain commented-out code.
src/pyVertexModel/geometry/geo.py:1026
This comment appears to contain commented-out code.
src/pyVertexModel/geometry/geo.py:1263
This comment appears to contain commented-out code.
src/pyVertexModel/geometry/geo.py:1517
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src/pyVertexModel/geometry/geo.py:2204
This comment appears to contain commented-out code.
src/pyVertexModel/Kg/kgContractility_external.py:37
This comment appears to contain commented-out code.

                # if currentFace.InterfaceType == 1 or currentFace.InterfaceType == 'Lateral':
                #     continue

src/pyVertexModel/main_paper_simulations.py:138

This comment appears to contain commented-out code.
src/pyVertexModel/main_paper_simulations.py:164
This comment appears to contain commented-out code.
src/pyVertexModel/algorithm/newtonRaphson.py:419
This comment appears to contain commented-out code.

    # if Set.InPlaneElasticity:
    #     gt, Kt, EBulk = KgBulk(geo_0, Geo, Set)
    #     K += Kt
    #     g += gt
    #     E += EBulk
    #     Energies["Bulk"] = EBulk

src/pyVertexModel/algorithm/newtonRaphson.py:526

This comment appears to contain commented-out code.

    # if Set.InPlaneElasticity:
    #     gt, Kt, EBulk = KgBulk(geo_0, Geo, Set)
    #     K += Kt
    #     g += gt
    #     E += EBulk
    #     Energies["Bulk"] = EBulk

src/pyVertexModel/mesh_remodelling/remodelling.py:395

This comment appears to contain commented-out code.
src/pyVertexModel/mesh_remodelling/remodelling.py:559
This comment appears to contain commented-out code.
src/pyVertexModel/algorithm/vertexModel.py:290
This comment appears to contain commented-out code.

            # if os.path.getmtime(output_filename) < (time.time() - 24 * 60 * 60):
            #     logger.info(f'Redoing the file {output_filename} as it is older than 1 day')
            # else:

src/pyVertexModel/algorithm/vertexModel.py:781

This comment appears to contain commented-out code.

        # except Exception as e:
        #     logger.error(f"Error while computing wound features: {e}")

src/pyVertexModel/algorithm/vertexModel.py:1160

This comment appears to contain commented-out code.

                #except Exception as e:
                #    logger.error(f'Error while running the iteration for purse string strength: {e}')
                #    return np.inf, np.inf, np.inf, np.inf

src/pyVertexModel/algorithm/vertexModelVoronoiFromTimeImage.py:365

This comment appears to contain commented-out code.
src/pyVertexModel/algorithm/vertexModelVoronoiFromTimeImage.py:423
This comment appears to contain commented-out code.
Tests/test_degreesOfFreedom.py:33
Call to method DegreesOfFreedom.get_remodel_dofs with too few arguments; should be no fewer than 3.

        dof_test.get_remodel_dofs(t_new_test, geo_test)

Tests/test_flip.py:29

Call to function y_flip_nm with too few arguments; should be no fewer than 7.

        tnew_test, _ = y_flip_nm(old_tets, cell_to_intercalate_with, old_ys, xs_to_disconnect, geo_test, set_test)

Tests/test_flip.py:50

Call to function y_flip_nm with too few arguments; should be no fewer than 7.

        tnew_test, _ = y_flip_nm(old_tets, cell_to_intercalate_with, old_ys, xs_to_disconnect, geo_test, set_test)

Tests/test_flip.py:120

Call to function post_flip with too many arguments; should be no more than 9.

        _, _, geo_test, _, _, _ = post_flip(Tnew, Ynew, oldTets, geo_test, geo_n, geo_0, Dofs, newYgIds, set_test,
                                            '-', segmentToChange)

Tests/test_flip.py:144

Call to function post_flip with too many arguments; should be no more than 9.

        _, _, geo_test, _, _, _ = post_flip(Tnew, Ynew, oldTets, geo_test, geo_n, geo_0, Dofs, newYgIds, set_test,
                                            '-', segmentToChange)

Tests/test_geo.py:202

Call to method Geo.check_ys_and_faces_have_not_changed with too few arguments; should be no fewer than 3.

        geo_test.check_ys_and_faces_have_not_changed(new_tets_test, old_geo_test)

Tests/test_geo.py:233

Call to method Geo.check_ys_and_faces_have_not_changed with too few arguments; should be no fewer than 3.

        geo_test.check_ys_and_faces_have_not_changed(new_tets_test, old_geo_test)

Tests/test_remodelling.py:33

Call to method Remodelling.intercalate_cells with too many arguments; should be no more than 1.

         ghost_nodes_tried, hasConverged, newYgIds) = remodelling_test.intercalate_cells(newYgIds, segmentFeatures)

src/pyVertexModel/algorithm/VertexModelVoronoi3D.py:116

Variable Twg_numPlane is not used.

            Twg_numPlane = create_tetrahedra(triangles_connectivity, neighbours_network, cell_edges,

src/pyVertexModel/mesh_remodelling/flip.py:273

Variable ys_4_cells is not used.
src/pyVertexModel/geometry/geo.py:549
Variable avg_faces is not used.
src/pyVertexModel/geometry/geo.py:2006
Variable original_tets is not used.
src/pyVertexModel/Kg/kgVolume.py:19
Variable dim is not used.

    dim = 3

src/pyVertexModel/util/space_exploration.py:114

Variable in_vivo_values_height is not used.
src/pyVertexModel/util/space_exploration.py:141
Variable all_files_features is not used.
Tests/test_vertexModel.py:294
Variable x is not used.

        x = mat_info['X']

src/pyVertexModel/algorithm/vertexModelBubbles.py:433

Variable X_IDs is not used.
src/pyVertexModel/analysis/analyse_pre_ablation_state.py:19
This assignment to 'file_name' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/analysis/analyse_simulation.py:79
This assignment to 'important_features' is unnecessary as it is redefined before this value is used.
This assignment to 'important_features' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/analysis/analyse_simulation.py:80
This assignment to 'post_wound_features' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/main.py:35
This assignment to 'name_last_pkl_file' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/analysis/obtain_vtks_from_file.py:73
This assignment to 'specific_files' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/mesh_remodelling/remodelling.py:338
This assignment to 'num_step' is unnecessary as it is redefined before this value is used.
src/pyVertexModel/mesh_remodelling/remodelling.py:347
This assignment to 'num_step' is unnecessary as it is redefined before this value is used.
Tests/test_vertexModel.py:516
Keyword argument 'set_option' is not a supported parameter name of Set.init.

        set_test = Set(set_option='voronoi_from_image')

Tests/test_vertexModel.py:566

Keyword argument 'set_option' is not a supported parameter name of Set.init.

        set_test = Set(set_option='voronoi_from_image')

src/pyVertexModel/geometry/geo.py:1363

Except block directly handles BaseException.
src/pyVertexModel/analysis/analyse_simulation.py:182
'except' clause does nothing but pass and there is no explanatory comment.
src/pyVertexModel/analysis/obtain_best_parameters.py:29
'except' clause does nothing but pass and there is no explanatory comment.
src/pyVertexModel/analysis/obtain_best_parameters.py:34
'except' clause does nothing but pass and there is no explanatory comment.
src/pyVertexModel/Kg/kgContractility.py:222
Unnecessary 'pass' statement.

                                pass

src/pyVertexModel/main.py:55

This statement is unreachable.
src/pyVertexModel/analysis/obtain_vtks_from_file.py:20
This statement is unreachable.
src/pyVertexModel/algorithm/vertexModel.py:94
This statement is unreachable.

        z_coordinate = [cell_height, -cell_height]

Tests/test_flip.py:29

Left hand side of assignment contains 2 variables, but right hand side is a tuple of length 3.

        tnew_test, _ = y_flip_nm(old_tets, cell_to_intercalate_with, old_ys, xs_to_disconnect, geo_test, set_test)

Tests/test_flip.py:50

Left hand side of assignment contains 2 variables, but right hand side is a tuple of length 3.

        tnew_test, _ = y_flip_nm(old_tets, cell_to_intercalate_with, old_ys, xs_to_disconnect, geo_test, set_test)

Tests/test_flip.py:120

Left hand side of assignment contains 6 variables, but right hand side is a tuple of length 5.

        _, _, geo_test, _, _, _ = post_flip(Tnew, Ynew, oldTets, geo_test, geo_n, geo_0, Dofs, newYgIds, set_test,
                                            '-', segmentToChange)

Tests/test_flip.py:144

Left hand side of assignment contains 6 variables, but right hand side is a tuple of length 5.

        _, _, geo_test, _, _, _ = post_flip(Tnew, Ynew, oldTets, geo_test, geo_n, geo_0, Dofs, newYgIds, set_test,
                                            '-', segmentToChange)

Copilot · 2026-02-04T10:08:02Z

src/pyVertexModel/__init__.py

+__all__ = ["PROJECT_DIRECTORY"]
+


The all variable is defined twice (lines 13 and 38). The first definition only includes "PROJECT_DIRECTORY" while the second includes 'version', 'PROJECT_DIRECTORY', and 'logger'. Remove the first definition on line 13 as it is incomplete and will be overwritten by line 38.

Suggested change

__all__ = ["PROJECT_DIRECTORY"]

Copilot · 2026-02-04T10:08:03Z

src/pyVertexModel/algorithm/vertexModel.py

 logger = logging.getLogger("pyVertexModel")
-
-
+PROJECT_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))


PROJECT_DIRECTORY is being redefined locally and will point to the wrong directory. This definition creates a path pointing to 'src/pyVertexModel/' instead of the project root. Since PROJECT_DIRECTORY is now properly exported from 'pyVertexModel.init', this local redefinition should be removed. The code on line 274 (os.path.join(PROJECT_DIRECTORY, self.set.initial_filename_state)) expects PROJECT_DIRECTORY to be the project root, not the pyVertexModel subdirectory.

Copilot · 2026-02-04T10:08:03Z

src/pyVertexModel/algorithm/vertexModelVoronoiFromTimeImage.py

+
+
+logger = logging.getLogger("pyVertexModel")
+PROJECT_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))


PROJECT_DIRECTORY is being redefined locally and will point to the wrong directory. This definition creates a path pointing to 'src/pyVertexModel/' instead of the project root. Since PROJECT_DIRECTORY is now properly exported from 'pyVertexModel.init', this local redefinition should be removed. The code on line 581 (PROJECT_DIRECTORY + '/' + self.set.initial_filename_state) expects PROJECT_DIRECTORY to be the project root, not the pyVertexModel subdirectory.

Copilot · 2026-02-04T10:08:03Z

src/pyVertexModel/analysis/analyse_optuna_results.py

@@ -8,8 +8,8 @@
 import seaborn as sns
 from scipy.optimize import curve_fit


Import of 'curve_fit' is not used.

Copilot · 2026-02-04T10:08:03Z

src/pyVertexModel/analysis/analyse_simulation.py

-from src.pyVertexModel.algorithm.vertexModel import VertexModel, logger
-from src.pyVertexModel.util.utils import load_state, load_variables, save_variables, screenshot
+from pyVertexModel.algorithm.vertexModel import VertexModel, logger
+from pyVertexModel.util.utils import load_state, load_variables, save_variables, screenshot


Import of 'screenshot' is not used.

Copilot · 2026-02-04T10:08:04Z

src/pyVertexModel/analysis/analyse_simulations.py


-from src.pyVertexModel.analysis.analyse_simulation import analyse_simulation, create_video
-from src.pyVertexModel.util.utils import plot_figure_with_line
+from pyVertexModel.analysis.analyse_simulation import analyse_simulation, create_video


Import of 'create_video' is not used.

Copilot · 2026-02-04T10:08:04Z

src/pyVertexModel/analysis/analysis_megha.py

+from pyVertexModel.Kg.kgVolume import KgVolume
+from pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import VertexModelVoronoiFromTimeImage
+from pyVertexModel.geometry.cell import compute_2d_circularity
+from pyVertexModel.util.utils import load_state, save_variables, load_variables, screenshot


Import of 'screenshot' is not used.

Copilot · 2026-02-04T10:08:04Z

src/pyVertexModel/main.py

-from src.pyVertexModel.util.utils import load_state
+from pyVertexModel import PROJECT_DIRECTORY
+from pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import VertexModelVoronoiFromTimeImage
+from pyVertexModel.analysis.analyse_simulation import analyse_simulation


Import of 'analyse_simulation' is not used.

Copilot · 2026-02-04T10:08:04Z

src/pyVertexModel/main_optuna.py

-from src import PROJECT_DIRECTORY
-from src.pyVertexModel.util.space_exploration import objective, plot_optuna_all, load_simulations, create_study_name
+from pyVertexModel import PROJECT_DIRECTORY
+from pyVertexModel.util.space_exploration import objective, plot_optuna_all, load_simulations, create_study_name


Import of 'load_simulations' is not used.

Initial plan

05e5994

Copilot AI assigned Copilot and Pablo1990 Feb 3, 2026

Copilot started work on behalf of Pablo1990 February 3, 2026 16:08 View session

Copilot AI and others added 3 commits February 3, 2026 16:13

Remove 'src' from imports - update setup.py, imports, and package str…

ff2e7fd

…ucture Co-authored-by: Pablo1990 <1974224+Pablo1990@users.noreply.github.com>

Fix remaining src imports and remove obsolete src/__init__.py

29fed39

Co-authored-by: Pablo1990 <1974224+Pablo1990@users.noreply.github.com>

Use pathlib for clearer PROJECT_DIRECTORY calculation

799ac02

Co-authored-by: Pablo1990 <1974224+Pablo1990@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Fix project import process to exclude 'src' directory~~ Remove 'src' prefix from imports - standardize package structure Feb 3, 2026

Copilot AI requested a review from Pablo1990 February 3, 2026 16:19

Copilot finished work on behalf of Pablo1990 February 3, 2026 16:19

Pablo1990 added 2 commits February 4, 2026 10:35

Removing GUI

6a46668

Review done

534987a

don't check in pull requests just after push

2ef3ddf

Pablo1990 marked this pull request as ready for review February 4, 2026 10:02

Copilot AI review requested due to automatic review settings February 4, 2026 10:02

Pablo1990 merged commit 44a7ed3 into main Feb 4, 2026
4 checks passed

Pablo1990 deleted the copilot/fix-import-project-src branch February 4, 2026 10:02

Copilot started reviewing on behalf of Pablo1990 February 4, 2026 10:02 View session

Copilot AI reviewed Feb 4, 2026

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Remove 'src' prefix from imports - standardize package structure#17

Remove 'src' prefix from imports - standardize package structure#17
Pablo1990 merged 7 commits intomainfrom
copilot/fix-import-project-src

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		logger = logging.getLogger("pyVertexModel")


		PROJECT_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))

		@@ -8,8 +8,8 @@
		import seaborn as sns
		from scipy.optimize import curve_fit

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