updated install setup

CosmoStat · Oct 11, 2024 · 1462605 · 1462605
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Showing 104 changed files with 45 additions and 35 deletions.
diff --git a/.github/workflows/ci-dev.yml b/.github/workflows/ci-dev.yml
@@ -15,10 +15,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8]
+        python-version: [3.11]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout
 
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
@@ -37,6 +37,7 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           auto-activate-base: true
+          miniforge-version: latest
 
       - name: Install package
         shell: bash -l {0}
@@ -47,5 +48,5 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate shapepipe-dev
-          python setup.py test
+          pytest
           shapepipe_run -c example/config.ini
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,29 @@
+[project]
+name = "shapepipe"
+version = "1.0.2"
+description = "Galaxy shape measurement pipeline."
+authors = [
+    { name = "Samuel Farrens", email = "samuel.farrens@cea.fr" },
+    { name = "Axel Guinot", email = "axel.guinot@cea.fr" },
+    { name = "Martin Kilbinger", email = "martin.kilbinger@cea.fr" }
+]
+dependencies = [
+    "joblib>=0.13",
+    "modopt>=1.2",
+    "numpy>=1.14"
+]
+
+[project.optional-dependencies]
+testing = [
+    "pytest",
+    "pytest-cov",
+    "pytest-pycodestyle",
+    "pytest-pydocstyle"
+]
+
+[project.scripts]
+shapepipe_run = "shapepipe.shapepipe_run:main"
+
+[tool.pytest.ini_options]
+addopts = "--verbose --cov=shapepipe"
+testpaths = ["shapepipe"]
diff --git a/setup.cfg → setup.cfg.old b/setup.cfg → setup.cfg.old
diff --git a/setup.py → setup.py.old b/setup.py → setup.py.old
diff --git a/shapepipe/__init__.py → src/shapepipe/__init__.py b/shapepipe/__init__.py → src/shapepipe/__init__.py
@@ -8,5 +8,8 @@
 
 __all__ = ['modules', 'pipeline', 'utilities']
 
+from importlib.metadata import metadata, version
 from . import *
-from .info import __about__, __version__
+
+__version__ = version("shapepipe")
+__about__ = metadata("shapepipe").get("Summary")
diff --git a/shapepipe/info.py → src/shapepipe/info.py b/shapepipe/info.py → src/shapepipe/info.py
@@ -12,33 +12,8 @@
     import_fail = True
 else:
     import_fail = False
-
-
-# Package Info
-version_info = (1, 0, 1)
-__version__ = '.'.join(str(c) for c in version_info)
-__name__ = 'shapepipe'
-__author__ = 'Samuel Farrens'
-__email__ = 'samuel.farrens@cea.fr'
-__about__ = (
-    'ShapePipe is a shape measurement pipeline developed with the'
-    + 'CosmoStat lab at CEA Paris-Saclay.'
-)
-__setups__ = ['pytest-runner']
-__installs__ = [
-    'joblib>=0.13',
-    'modopt>=1.2',
-    'numpy>=1.14'
-]
-__tests__ = [
-    'pytest',
-    'pytest-cov',
-    'pytest-pycodestyle',
-    'pytest-pydocstyle',
-]
-__scripts_dir__ = 'scripts'
-__scripts_ext__ = ('.py', '.sh', '.bash')
-
+
+from shapepipe import __version__
 
 def shapepipe_logo(colour=False):
     """Get ShapePipe Logo.

diff --git a/shapepipe/modules/__init__.py → src/shapepipe/modules/__init__.py b/shapepipe/modules/__init__.py → src/shapepipe/modules/__init__.py
diff --git a/shapepipe/modules/execute_example_runner.py → ...apepipe/modules/execute_example_runner.py b/shapepipe/modules/execute_example_runner.py → ...apepipe/modules/execute_example_runner.py
diff --git a/...odules/find_exposures_package/__init__.py → ...odules/find_exposures_package/__init__.py b/...odules/find_exposures_package/__init__.py → ...odules/find_exposures_package/__init__.py
diff --git a/.../find_exposures_package/find_exposures.py → .../find_exposures_package/find_exposures.py b/.../find_exposures_package/find_exposures.py → .../find_exposures_package/find_exposures.py
diff --git a/shapepipe/modules/find_exposures_runner.py → ...hapepipe/modules/find_exposures_runner.py b/shapepipe/modules/find_exposures_runner.py → ...hapepipe/modules/find_exposures_runner.py
diff --git a/...pe/modules/get_images_package/__init__.py → ...pe/modules/get_images_package/__init__.py b/...pe/modules/get_images_package/__init__.py → ...pe/modules/get_images_package/__init__.py
diff --git a/.../modules/get_images_package/get_images.py → .../modules/get_images_package/get_images.py b/.../modules/get_images_package/get_images.py → .../modules/get_images_package/get_images.py
diff --git a/shapepipe/modules/get_images_runner.py → src/shapepipe/modules/get_images_runner.py b/shapepipe/modules/get_images_runner.py → src/shapepipe/modules/get_images_runner.py
diff --git a/...pipe/modules/make_cat_package/__init__.py → ...pipe/modules/make_cat_package/__init__.py b/...pipe/modules/make_cat_package/__init__.py → ...pipe/modules/make_cat_package/__init__.py
diff --git a/...pipe/modules/make_cat_package/make_cat.py → ...pipe/modules/make_cat_package/make_cat.py b/...pipe/modules/make_cat_package/make_cat.py → ...pipe/modules/make_cat_package/make_cat.py
diff --git a/shapepipe/modules/make_cat_runner.py → src/shapepipe/modules/make_cat_runner.py b/shapepipe/modules/make_cat_runner.py → src/shapepipe/modules/make_cat_runner.py
diff --git a/shapepipe/modules/mask_package/__init__.py → ...hapepipe/modules/mask_package/__init__.py b/shapepipe/modules/mask_package/__init__.py → ...hapepipe/modules/mask_package/__init__.py
diff --git a/shapepipe/modules/mask_package/mask.py → src/shapepipe/modules/mask_package/mask.py b/shapepipe/modules/mask_package/mask.py → src/shapepipe/modules/mask_package/mask.py
diff --git a/shapepipe/modules/mask_runner.py → src/shapepipe/modules/mask_runner.py b/shapepipe/modules/mask_runner.py → src/shapepipe/modules/mask_runner.py
diff --git a/...odules/match_external_package/__init__.py → ...odules/match_external_package/__init__.py b/...odules/match_external_package/__init__.py → ...odules/match_external_package/__init__.py
diff --git a/.../match_external_package/match_external.py → .../match_external_package/match_external.py b/.../match_external_package/match_external.py → .../match_external_package/match_external.py
diff --git a/shapepipe/modules/match_external_runner.py → ...hapepipe/modules/match_external_runner.py b/shapepipe/modules/match_external_runner.py → ...hapepipe/modules/match_external_runner.py
diff --git a/shapepipe/modules/mccd_fit_runner.py → src/shapepipe/modules/mccd_fit_runner.py b/shapepipe/modules/mccd_fit_runner.py → src/shapepipe/modules/mccd_fit_runner.py
diff --git a/shapepipe/modules/mccd_fit_val_runner.py → src/shapepipe/modules/mccd_fit_val_runner.py b/shapepipe/modules/mccd_fit_val_runner.py → src/shapepipe/modules/mccd_fit_val_runner.py
diff --git a/shapepipe/modules/mccd_interp_runner.py → src/shapepipe/modules/mccd_interp_runner.py b/shapepipe/modules/mccd_interp_runner.py → src/shapepipe/modules/mccd_interp_runner.py
diff --git a/shapepipe/modules/mccd_package/__init__.py → ...hapepipe/modules/mccd_package/__init__.py b/shapepipe/modules/mccd_package/__init__.py → ...hapepipe/modules/mccd_package/__init__.py
diff --git a/...mccd_package/mccd_interpolation_script.py → ...mccd_package/mccd_interpolation_script.py b/...mccd_package/mccd_interpolation_script.py → ...mccd_package/mccd_interpolation_script.py
diff --git a/...dules/mccd_package/mccd_plot_utilities.py → ...dules/mccd_package/mccd_plot_utilities.py b/...dules/mccd_package/mccd_plot_utilities.py → ...dules/mccd_package/mccd_plot_utilities.py
diff --git a/.../mccd_package/shapepipe_auxiliary_mccd.py → .../mccd_package/shapepipe_auxiliary_mccd.py b/.../mccd_package/shapepipe_auxiliary_mccd.py → .../mccd_package/shapepipe_auxiliary_mccd.py
diff --git a/shapepipe/modules/mccd_plots_runner.py → src/shapepipe/modules/mccd_plots_runner.py b/shapepipe/modules/mccd_plots_runner.py → src/shapepipe/modules/mccd_plots_runner.py
diff --git a/...pipe/modules/mccd_preprocessing_runner.py → ...pipe/modules/mccd_preprocessing_runner.py b/...pipe/modules/mccd_preprocessing_runner.py → ...pipe/modules/mccd_preprocessing_runner.py
diff --git a/shapepipe/modules/mccd_val_runner.py → src/shapepipe/modules/mccd_val_runner.py b/shapepipe/modules/mccd_val_runner.py → src/shapepipe/modules/mccd_val_runner.py
diff --git a/...modules/merge_headers_package/__init__.py → ...modules/merge_headers_package/__init__.py b/...modules/merge_headers_package/__init__.py → ...modules/merge_headers_package/__init__.py
diff --git a/...es/merge_headers_package/merge_headers.py → ...es/merge_headers_package/merge_headers.py b/...es/merge_headers_package/merge_headers.py → ...es/merge_headers_package/merge_headers.py
diff --git a/shapepipe/modules/merge_headers_runner.py → ...shapepipe/modules/merge_headers_runner.py b/shapepipe/modules/merge_headers_runner.py → ...shapepipe/modules/merge_headers_runner.py
diff --git a/...odules/merge_sep_cats_package/__init__.py → ...odules/merge_sep_cats_package/__init__.py b/...odules/merge_sep_cats_package/__init__.py → ...odules/merge_sep_cats_package/__init__.py
diff --git a/.../merge_sep_cats_package/merge_sep_cats.py → .../merge_sep_cats_package/merge_sep_cats.py b/.../merge_sep_cats_package/merge_sep_cats.py → .../merge_sep_cats_package/merge_sep_cats.py
diff --git a/shapepipe/modules/merge_sep_cats_runner.py → ...hapepipe/modules/merge_sep_cats_runner.py b/shapepipe/modules/merge_sep_cats_runner.py → ...hapepipe/modules/merge_sep_cats_runner.py
diff --git a/...modules/merge_starcat_package/__init__.py → ...modules/merge_starcat_package/__init__.py b/...modules/merge_starcat_package/__init__.py → ...modules/merge_starcat_package/__init__.py
diff --git a/...es/merge_starcat_package/merge_starcat.py → ...es/merge_starcat_package/merge_starcat.py b/...es/merge_starcat_package/merge_starcat.py → ...es/merge_starcat_package/merge_starcat.py
diff --git a/shapepipe/modules/merge_starcat_runner.py → ...shapepipe/modules/merge_starcat_runner.py b/shapepipe/modules/merge_starcat_runner.py → ...shapepipe/modules/merge_starcat_runner.py
diff --git a/shapepipe/modules/module_decorator.py → src/shapepipe/modules/module_decorator.py b/shapepipe/modules/module_decorator.py → src/shapepipe/modules/module_decorator.py
diff --git a/shapepipe/modules/module_runners.py → src/shapepipe/modules/module_runners.py b/shapepipe/modules/module_runners.py → src/shapepipe/modules/module_runners.py
diff --git a/shapepipe/modules/ngmix_package/__init__.py → ...apepipe/modules/ngmix_package/__init__.py b/shapepipe/modules/ngmix_package/__init__.py → ...apepipe/modules/ngmix_package/__init__.py
diff --git a/shapepipe/modules/ngmix_package/ngmix.py → src/shapepipe/modules/ngmix_package/ngmix.py b/shapepipe/modules/ngmix_package/ngmix.py → src/shapepipe/modules/ngmix_package/ngmix.py
diff --git a/shapepipe/modules/ngmix_runner.py → src/shapepipe/modules/ngmix_runner.py b/shapepipe/modules/ngmix_runner.py → src/shapepipe/modules/ngmix_runner.py
diff --git a/...pipe/modules/pastecat_package/__init__.py → ...pipe/modules/pastecat_package/__init__.py b/...pipe/modules/pastecat_package/__init__.py → ...pipe/modules/pastecat_package/__init__.py
diff --git a/...pipe/modules/pastecat_package/pastecat.py → ...pipe/modules/pastecat_package/pastecat.py b/...pipe/modules/pastecat_package/pastecat.py → ...pipe/modules/pastecat_package/pastecat.py
diff --git a/shapepipe/modules/pastecat_runner.py → src/shapepipe/modules/pastecat_runner.py b/shapepipe/modules/pastecat_runner.py → src/shapepipe/modules/pastecat_runner.py
diff --git a/.../modules/psfex_interp_package/__init__.py → .../modules/psfex_interp_package/__init__.py b/.../modules/psfex_interp_package/__init__.py → .../modules/psfex_interp_package/__init__.py
diff --git a/...ules/psfex_interp_package/psfex_interp.py → ...ules/psfex_interp_package/psfex_interp.py b/...ules/psfex_interp_package/psfex_interp.py → ...ules/psfex_interp_package/psfex_interp.py
diff --git a/shapepipe/modules/psfex_interp_runner.py → src/shapepipe/modules/psfex_interp_runner.py b/shapepipe/modules/psfex_interp_runner.py → src/shapepipe/modules/psfex_interp_runner.py
diff --git a/shapepipe/modules/psfex_package/__init__.py → ...apepipe/modules/psfex_package/__init__.py b/shapepipe/modules/psfex_package/__init__.py → ...apepipe/modules/psfex_package/__init__.py
diff --git a/...ipe/modules/psfex_package/psfex_script.py → ...ipe/modules/psfex_package/psfex_script.py b/...ipe/modules/psfex_package/psfex_script.py → ...ipe/modules/psfex_package/psfex_script.py
diff --git a/shapepipe/modules/psfex_runner.py → src/shapepipe/modules/psfex_runner.py b/shapepipe/modules/psfex_runner.py → src/shapepipe/modules/psfex_runner.py
diff --git a/...odules/python_example_package/__init__.py → ...odules/python_example_package/__init__.py b/...odules/python_example_package/__init__.py → ...odules/python_example_package/__init__.py
diff --git a/.../python_example_package/python_example.py → .../python_example_package/python_example.py b/.../python_example_package/python_example.py → .../python_example_package/python_example.py
diff --git a/shapepipe/modules/python_example_runner.py → ...hapepipe/modules/python_example_runner.py b/shapepipe/modules/python_example_runner.py → ...hapepipe/modules/python_example_runner.py
diff --git a/...pe/modules/random_cat_package/__init__.py → ...pe/modules/random_cat_package/__init__.py b/...pe/modules/random_cat_package/__init__.py → ...pe/modules/random_cat_package/__init__.py
diff --git a/.../modules/random_cat_package/random_cat.py → .../modules/random_cat_package/random_cat.py b/.../modules/random_cat_package/random_cat.py → .../modules/random_cat_package/random_cat.py
diff --git a/shapepipe/modules/random_cat_runner.py → src/shapepipe/modules/random_cat_runner.py b/shapepipe/modules/random_cat_runner.py → src/shapepipe/modules/random_cat_runner.py
diff --git a/shapepipe/modules/serial_example_runner.py → ...hapepipe/modules/serial_example_runner.py b/shapepipe/modules/serial_example_runner.py → ...hapepipe/modules/serial_example_runner.py
diff --git a/...epipe/modules/setools_package/__init__.py → ...epipe/modules/setools_package/__init__.py b/...epipe/modules/setools_package/__init__.py → ...epipe/modules/setools_package/__init__.py
diff --git a/shapepipe/modules/setools_package/setools.py → ...pepipe/modules/setools_package/setools.py b/shapepipe/modules/setools_package/setools.py → ...pepipe/modules/setools_package/setools.py
diff --git a/shapepipe/modules/setools_runner.py → src/shapepipe/modules/setools_runner.py b/shapepipe/modules/setools_runner.py → src/shapepipe/modules/setools_runner.py
diff --git a/...pe/modules/sextractor_package/__init__.py → ...pe/modules/sextractor_package/__init__.py b/...pe/modules/sextractor_package/__init__.py → ...pe/modules/sextractor_package/__init__.py
diff --git a/...s/sextractor_package/sextractor_script.py → ...s/sextractor_package/sextractor_script.py b/...s/sextractor_package/sextractor_script.py → ...s/sextractor_package/sextractor_script.py
diff --git a/shapepipe/modules/sextractor_runner.py → src/shapepipe/modules/sextractor_runner.py b/shapepipe/modules/sextractor_runner.py → src/shapepipe/modules/sextractor_runner.py
diff --git a/...ipe/modules/split_exp_package/__init__.py → ...ipe/modules/split_exp_package/__init__.py b/...ipe/modules/split_exp_package/__init__.py → ...ipe/modules/split_exp_package/__init__.py
diff --git a/...pe/modules/split_exp_package/split_exp.py → ...pe/modules/split_exp_package/split_exp.py b/...pe/modules/split_exp_package/split_exp.py → ...pe/modules/split_exp_package/split_exp.py
diff --git a/shapepipe/modules/split_exp_runner.py → src/shapepipe/modules/split_exp_runner.py b/shapepipe/modules/split_exp_runner.py → src/shapepipe/modules/split_exp_runner.py
diff --git a/.../modules/spread_model_package/__init__.py → .../modules/spread_model_package/__init__.py b/.../modules/spread_model_package/__init__.py → .../modules/spread_model_package/__init__.py
diff --git a/...ules/spread_model_package/spread_model.py → ...ules/spread_model_package/spread_model.py b/...ules/spread_model_package/spread_model.py → ...ules/spread_model_package/spread_model.py
diff --git a/shapepipe/modules/spread_model_runner.py → src/shapepipe/modules/spread_model_runner.py b/shapepipe/modules/spread_model_runner.py → src/shapepipe/modules/spread_model_runner.py
diff --git a/...dules/uncompress_fits_package/__init__.py → ...dules/uncompress_fits_package/__init__.py b/...dules/uncompress_fits_package/__init__.py → ...dules/uncompress_fits_package/__init__.py
diff --git a/...ncompress_fits_package/uncompress_fits.py → ...ncompress_fits_package/uncompress_fits.py b/...ncompress_fits_package/uncompress_fits.py → ...ncompress_fits_package/uncompress_fits.py
diff --git a/shapepipe/modules/uncompress_fits_runner.py → ...apepipe/modules/uncompress_fits_runner.py b/shapepipe/modules/uncompress_fits_runner.py → ...apepipe/modules/uncompress_fits_runner.py
diff --git a/...e/modules/vignetmaker_package/__init__.py → ...e/modules/vignetmaker_package/__init__.py b/...e/modules/vignetmaker_package/__init__.py → ...e/modules/vignetmaker_package/__init__.py
diff --git a/...odules/vignetmaker_package/vignetmaker.py → ...odules/vignetmaker_package/vignetmaker.py b/...odules/vignetmaker_package/vignetmaker.py → ...odules/vignetmaker_package/vignetmaker.py
diff --git a/shapepipe/modules/vignetmaker_runner.py → src/shapepipe/modules/vignetmaker_runner.py b/shapepipe/modules/vignetmaker_runner.py → src/shapepipe/modules/vignetmaker_runner.py
diff --git a/shapepipe/pipeline/__init__.py → src/shapepipe/pipeline/__init__.py b/shapepipe/pipeline/__init__.py → src/shapepipe/pipeline/__init__.py
diff --git a/shapepipe/pipeline/args.py → src/shapepipe/pipeline/args.py b/shapepipe/pipeline/args.py → src/shapepipe/pipeline/args.py
@@ -8,7 +8,8 @@
 
 import argparse as ap
 
-from shapepipe.info import __version__, shapepipe_logo
+from shapepipe import __version__
+from shapepipe.info import shapepipe_logo
 from shapepipe.modules import __module_list__
 
 

diff --git a/shapepipe/pipeline/config.py → src/shapepipe/pipeline/config.py b/shapepipe/pipeline/config.py → src/shapepipe/pipeline/config.py
diff --git a/shapepipe/pipeline/dependency_handler.py → src/shapepipe/pipeline/dependency_handler.py b/shapepipe/pipeline/dependency_handler.py → src/shapepipe/pipeline/dependency_handler.py
diff --git a/shapepipe/pipeline/execute.py → src/shapepipe/pipeline/execute.py b/shapepipe/pipeline/execute.py → src/shapepipe/pipeline/execute.py
diff --git a/shapepipe/pipeline/file_handler.py → src/shapepipe/pipeline/file_handler.py b/shapepipe/pipeline/file_handler.py → src/shapepipe/pipeline/file_handler.py
diff --git a/shapepipe/pipeline/file_io.py → src/shapepipe/pipeline/file_io.py b/shapepipe/pipeline/file_io.py → src/shapepipe/pipeline/file_io.py
diff --git a/shapepipe/pipeline/job_handler.py → src/shapepipe/pipeline/job_handler.py b/shapepipe/pipeline/job_handler.py → src/shapepipe/pipeline/job_handler.py
diff --git a/shapepipe/pipeline/mpi_run.py → src/shapepipe/pipeline/mpi_run.py b/shapepipe/pipeline/mpi_run.py → src/shapepipe/pipeline/mpi_run.py
diff --git a/shapepipe/pipeline/run_log.py → src/shapepipe/pipeline/run_log.py b/shapepipe/pipeline/run_log.py → src/shapepipe/pipeline/run_log.py
diff --git a/shapepipe/pipeline/shared.py → src/shapepipe/pipeline/shared.py b/shapepipe/pipeline/shared.py → src/shapepipe/pipeline/shared.py
diff --git a/shapepipe/pipeline/str_handler.py → src/shapepipe/pipeline/str_handler.py b/shapepipe/pipeline/str_handler.py → src/shapepipe/pipeline/str_handler.py
diff --git a/shapepipe/pipeline/timeout.py → src/shapepipe/pipeline/timeout.py b/shapepipe/pipeline/timeout.py → src/shapepipe/pipeline/timeout.py
diff --git a/shapepipe/pipeline/worker_handler.py → src/shapepipe/pipeline/worker_handler.py b/shapepipe/pipeline/worker_handler.py → src/shapepipe/pipeline/worker_handler.py
diff --git a/shapepipe/run.py → src/shapepipe/run.py b/shapepipe/run.py → src/shapepipe/run.py
@@ -8,12 +8,13 @@
 
 import sys
 from datetime import datetime
+from importlib.metadata import requires
 
 from joblib import cpu_count
 from modopt.interface.errors import catch_error
 from modopt.interface.log import close_log, set_up_log
 
-from shapepipe.info import __installs__, line, shapepipe_logo
+from shapepipe.info import line, shapepipe_logo
 from shapepipe.pipeline.args import create_arg_parser
 from shapepipe.pipeline.config import create_config_parser
 from shapepipe.pipeline.dependency_handler import DependencyHandler
@@ -172,9 +173,9 @@ def _check_dependencies(self):
         Check that all pipeline dependencies have been installed.
 
         """
-        module_dep = self._get_module_depends('depends') + __installs__
+        module_dep = self._get_module_depends('depends') + [dep.split()[0] for dep in requires("ShapePipe") if "extra ==" not in dep]
         module_exe = self._get_module_depends('executes')
-
+        
         module_dep += ['mpi4py'] if import_mpi else module_dep
 
         dh = DependencyHandler(module_dep, module_exe)

diff --git a/scripts/python/shapepipe_run.py → src/shapepipe/shapepipe_run.py b/scripts/python/shapepipe_run.py → src/shapepipe/shapepipe_run.py
diff --git a/shapepipe/tests/test_get_images.py → src/shapepipe/tests/test_get_images.py b/shapepipe/tests/test_get_images.py → src/shapepipe/tests/test_get_images.py
diff --git a/shapepipe/tests/test_pipeline.py → src/shapepipe/tests/test_pipeline.py b/shapepipe/tests/test_pipeline.py → src/shapepipe/tests/test_pipeline.py
diff --git a/shapepipe/tests/test_utilities.py → src/shapepipe/tests/test_utilities.py b/shapepipe/tests/test_utilities.py → src/shapepipe/tests/test_utilities.py
diff --git a/shapepipe/utilities/__init__.py → src/shapepipe/utilities/__init__.py b/shapepipe/utilities/__init__.py → src/shapepipe/utilities/__init__.py
diff --git a/shapepipe/utilities/cfis.py → src/shapepipe/utilities/cfis.py b/shapepipe/utilities/cfis.py → src/shapepipe/utilities/cfis.py
diff --git a/shapepipe/utilities/file_system.py → src/shapepipe/utilities/file_system.py b/shapepipe/utilities/file_system.py → src/shapepipe/utilities/file_system.py
diff --git a/shapepipe/utilities/galaxy.py → src/shapepipe/utilities/galaxy.py b/shapepipe/utilities/galaxy.py → src/shapepipe/utilities/galaxy.py