Reorganize (#19)

* reorganize repo * update pyproject * add missing files
haddocking · Apr 30, 2024 · 8bed487 · 8bed487
1 parent 8692d45
commit 8bed487
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Showing 15 changed files with 16 additions and 10 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git 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 → src/prodigy_cryst/__init__.py b/prodigy_cryst/__init__.py → src/prodigy_cryst/__init__.py
diff --git a/prodigy_cryst/classify.py → src/prodigy_cryst/classify.py b/prodigy_cryst/classify.py → src/prodigy_cryst/classify.py
diff --git a/prodigy_cryst/data/List_of_features-MANY.csv → ...digy_cryst/data/List_of_features-MANY.csv b/prodigy_cryst/data/List_of_features-MANY.csv → ...digy_cryst/data/List_of_features-MANY.csv
diff --git a/prodigy_cryst/data/classifier.sav → src/prodigy_cryst/data/classifier.sav b/prodigy_cryst/data/classifier.sav → src/prodigy_cryst/data/classifier.sav
diff --git a/prodigy_cryst/interface_classifier.py → src/prodigy_cryst/interface_classifier.py b/prodigy_cryst/interface_classifier.py → 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 → src/prodigy_cryst/modules/__init__.py b/prodigy_cryst/lib/__init__.py → src/prodigy_cryst/modules/__init__.py
diff --git a/prodigy_cryst/lib/aa_properties.py → src/prodigy_cryst/modules/aa_properties.py b/prodigy_cryst/lib/aa_properties.py → src/prodigy_cryst/modules/aa_properties.py
diff --git a/prodigy_cryst/lib/parsers.py → src/prodigy_cryst/modules/parsers.py b/prodigy_cryst/lib/parsers.py → src/prodigy_cryst/modules/parsers.py
diff --git a/prodigy_cryst/lib/utils.py → src/prodigy_cryst/modules/utils.py b/prodigy_cryst/lib/utils.py → src/prodigy_cryst/modules/utils.py
diff --git 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
@@ -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
@@ -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
@@ -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():