From 8bed487dab4990f6b7379e4c38669283194bf4e7 Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Tue, 30 Apr 2024 18:02:46 +0200 Subject: [PATCH] Reorganize (#19) * reorganize repo * update pyproject * add missing files --- poetry.lock | 4 ++-- pyproject.toml | 6 ++++++ {prodigy_cryst => src/prodigy_cryst}/__init__.py | 0 {prodigy_cryst => src/prodigy_cryst}/classify.py | 0 .../prodigy_cryst}/data/List_of_features-MANY.csv | 0 .../prodigy_cryst}/data/classifier.sav | Bin .../prodigy_cryst}/interface_classifier.py | 8 ++++---- .../lib => src/prodigy_cryst/modules}/__init__.py | 0 .../prodigy_cryst/modules}/aa_properties.py | 0 .../lib => src/prodigy_cryst/modules}/parsers.py | 0 .../lib => src/prodigy_cryst/modules}/utils.py | 0 tests/test_aa_properties.py | 2 +- tests/test_interface_classifier.py | 2 +- tests/test_parsers.py | 2 +- tests/test_utils.py | 2 +- 15 files changed, 16 insertions(+), 10 deletions(-) rename {prodigy_cryst => src/prodigy_cryst}/__init__.py (100%) rename {prodigy_cryst => src/prodigy_cryst}/classify.py (100%) rename {prodigy_cryst => src/prodigy_cryst}/data/List_of_features-MANY.csv (100%) rename {prodigy_cryst => src/prodigy_cryst}/data/classifier.sav (100%) rename {prodigy_cryst => src/prodigy_cryst}/interface_classifier.py (98%) rename {prodigy_cryst/lib => src/prodigy_cryst/modules}/__init__.py (100%) rename {prodigy_cryst/lib => src/prodigy_cryst/modules}/aa_properties.py (100%) rename {prodigy_cryst/lib => src/prodigy_cryst/modules}/parsers.py (100%) rename {prodigy_cryst/lib => src/prodigy_cryst/modules}/utils.py (100%) diff --git a/poetry.lock b/poetry.lock index e957bd5..85039e0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -404,5 +404,5 @@ files = [ [metadata] lock-version = "2.0" -python-versions = "~3.8,<3.9" -content-hash = "811c773f73bfc8dda34ee3bb804c9fa4f35b9cea6e2a08cd029061596c0aec29" +python-versions = ">=3.8,<3.9" +content-hash = "9c22e6e498b8212ae5fbb28e793134668e75084777101234af4c9822ebf4289c" diff --git a/pyproject.toml b/pyproject.toml index a6b2dde..b3990b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,12 @@ hypothesis = "^6.100.2" [tool.poetry.scripts] prodigy_cryst = "prodigy_cryst.interface_classifier:main" +[tool.setuptools] +include-package-data = true +packages = ["src"] + +[tool.pytest.ini_options] +pythonpath = ["src"] [build-system] requires = ["poetry-core"] diff --git a/prodigy_cryst/__init__.py b/src/prodigy_cryst/__init__.py similarity index 100% rename from prodigy_cryst/__init__.py rename to src/prodigy_cryst/__init__.py diff --git a/prodigy_cryst/classify.py b/src/prodigy_cryst/classify.py similarity index 100% rename from prodigy_cryst/classify.py rename to src/prodigy_cryst/classify.py diff --git a/prodigy_cryst/data/List_of_features-MANY.csv b/src/prodigy_cryst/data/List_of_features-MANY.csv similarity index 100% rename from prodigy_cryst/data/List_of_features-MANY.csv rename to src/prodigy_cryst/data/List_of_features-MANY.csv diff --git a/prodigy_cryst/data/classifier.sav b/src/prodigy_cryst/data/classifier.sav similarity index 100% rename from prodigy_cryst/data/classifier.sav rename to src/prodigy_cryst/data/classifier.sav diff --git a/prodigy_cryst/interface_classifier.py b/src/prodigy_cryst/interface_classifier.py similarity index 98% rename from prodigy_cryst/interface_classifier.py rename to src/prodigy_cryst/interface_classifier.py index 02cf43b..73950d0 100755 --- a/prodigy_cryst/interface_classifier.py +++ b/src/prodigy_cryst/interface_classifier.py @@ -27,11 +27,11 @@ logging.error("[!] The interface classifier tool requires Biopython") raise ImportError(e) -from prodigy_cryst.lib import aa_properties -from prodigy_cryst.lib.parsers import parse_structure +from prodigy_cryst.modules import aa_properties +from prodigy_cryst.modules.parsers import parse_structure # from prodigy_cryst.lib.freesasa import execute_freesasa -from prodigy_cryst.lib.utils import _check_path +from prodigy_cryst.modules.utils import _check_path def calculate_ic(structure, d_cutoff=5.0, selection=None): @@ -99,7 +99,7 @@ def analyse_contacts(contact_list): } _data = aa_properties.aa_character_ic - for (res_i, res_j) in contact_list: + for res_i, res_j in contact_list: contact_type = (_data.get(res_i.resname), _data.get(res_j.resname)) contact_type = "".join(sorted(contact_type)) bins[contact_type] += 1 diff --git a/prodigy_cryst/lib/__init__.py b/src/prodigy_cryst/modules/__init__.py similarity index 100% rename from prodigy_cryst/lib/__init__.py rename to src/prodigy_cryst/modules/__init__.py diff --git a/prodigy_cryst/lib/aa_properties.py b/src/prodigy_cryst/modules/aa_properties.py similarity index 100% rename from prodigy_cryst/lib/aa_properties.py rename to src/prodigy_cryst/modules/aa_properties.py diff --git a/prodigy_cryst/lib/parsers.py b/src/prodigy_cryst/modules/parsers.py similarity index 100% rename from prodigy_cryst/lib/parsers.py rename to src/prodigy_cryst/modules/parsers.py diff --git a/prodigy_cryst/lib/utils.py b/src/prodigy_cryst/modules/utils.py similarity index 100% rename from prodigy_cryst/lib/utils.py rename to src/prodigy_cryst/modules/utils.py diff --git a/tests/test_aa_properties.py b/tests/test_aa_properties.py index 5a48646..bcfe7b2 100644 --- a/tests/test_aa_properties.py +++ b/tests/test_aa_properties.py @@ -1,6 +1,6 @@ import pytest -from prodigy_cryst.lib.aa_properties import ( +from prodigy_cryst.modules.aa_properties import ( aa_character_ic, aa_character_protorp, rel_asa, diff --git a/tests/test_interface_classifier.py b/tests/test_interface_classifier.py index 7e8fa6e..5a6df83 100644 --- a/tests/test_interface_classifier.py +++ b/tests/test_interface_classifier.py @@ -9,7 +9,7 @@ analyse_contacts, calculate_ic, ) -from prodigy_cryst.lib.parsers import parse_structure +from prodigy_cryst.modules.parsers import parse_structure from tests import DATA_FOLDER diff --git a/tests/test_parsers.py b/tests/test_parsers.py index 05606a9..d07dfd2 100644 --- a/tests/test_parsers.py +++ b/tests/test_parsers.py @@ -3,7 +3,7 @@ import pytest from Bio.PDB.Structure import Structure -from prodigy_cryst.lib.parsers import parse_structure +from prodigy_cryst.modules.parsers import parse_structure from . import DATA_FOLDER diff --git a/tests/test_utils.py b/tests/test_utils.py index 9f1fa1c..ec6b076 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,6 +1,6 @@ from tempfile import NamedTemporaryFile -from prodigy_cryst.lib.utils import _check_path +from prodigy_cryst.modules.utils import _check_path def test__check_path():