Merge pull request #116 from volkamerlab/enable-klifs-only-installation

Remove io __init__ imports (to enable OpenCADD-KLIFS only deps)
volkamerlab · Nov 1, 2021 · 0a2b80d · 0a2b80d
2 parents ce20b50 + 949b6c4
commit 0a2b80d
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Showing 9 changed files with 12 additions and 12 deletions.
diff --git a/docs/tutorials/io.ipynb b/docs/tutorials/io.ipynb
@@ -35,7 +35,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from opencadd.io import DataFrame, Rdkit, Biopython"
+    "from opencadd.io.dataframe import DataFrame\n",
+    "from opencadd.io.rdkit import Rdkit\n",
+    "from opencadd.io.biopython import Biopython\n"
    ]
   },
   {

diff --git a/opencadd/databases/klifs/local.py b/opencadd/databases/klifs/local.py
@@ -30,7 +30,8 @@
 from .utils import PATH_DATA, metadata_to_filepath, filepath_to_metadata
 from .remote import KLIFS_CLIENT
 from .exceptions import KlifsPocketIncompleteError, KlifsPocketUnequalSequenceStructure
-from opencadd.io import DataFrame, Rdkit
+from opencadd.io.dataframe import DataFrame
+from opencadd.io.rdkit import Rdkit
 
 # Get the newest file version (* = YYYYMMDD)
 PATH_TO_KLIFS_IDS = sorted(PATH_DATA.glob("klifs_ids.*.csv.gz"), key=lambda x: x.suffixes[0])[-1]

diff --git a/opencadd/databases/klifs/remote.py b/opencadd/databases/klifs/remote.py
@@ -25,7 +25,8 @@
 )
 from .schema import FIELDS
 from .utils import metadata_to_filepath, silence_logging
-from opencadd.io import DataFrame, Rdkit
+from opencadd.io.dataframe import DataFrame
+from opencadd.io.rdkit import Rdkit
 
 _logger = logging.getLogger(__name__)
 

diff --git a/opencadd/io/__init__.py b/opencadd/io/__init__.py
@@ -1,7 +1,3 @@
 """
 opencadd.io module
 """
-
-from .biopython import Biopython
-from .dataframe import DataFrame
-from .rdkit import Rdkit
diff --git a/opencadd/structure/pocket/core.py b/opencadd/structure/pocket/core.py
@@ -8,7 +8,7 @@
 from pathlib import Path
 
 import pandas as pd
-from opencadd.io import DataFrame
+from opencadd.io.dataframe import DataFrame
 
 from .base import PocketBase
 from .features.region import Region

diff --git a/opencadd/structure/pocket/viewer.py b/opencadd/structure/pocket/viewer.py
@@ -9,7 +9,7 @@
 from matplotlib import colors
 import nglview
 
-from opencadd.io import DataFrame
+from opencadd.io.dataframe import DataFrame
 
 _logger = logging.getLogger(__name__)
 

diff --git a/opencadd/tests/io/test_biopython.py b/opencadd/tests/io/test_biopython.py
@@ -7,7 +7,7 @@
 import pytest
 from Bio.PDB.Structure import Structure
 
-from opencadd.io import Biopython
+from opencadd.io.biopython import Biopython
 
 PATH_TEST_DATA = Path(__name__).parent / "opencadd" / "tests" / "data" / "io"
 

diff --git a/opencadd/tests/io/test_dataframes.py b/opencadd/tests/io/test_dataframes.py
@@ -7,7 +7,7 @@
 import pandas as pd
 import pytest
 
-from opencadd.io import DataFrame
+from opencadd.io.dataframe import DataFrame
 from opencadd.io.schema import DATAFRAME_COLUMNS
 
 PATH_TEST_DATA = Path(__name__).parent / "opencadd" / "tests" / "data" / "io"

diff --git a/opencadd/tests/io/test_rdkit.py b/opencadd/tests/io/test_rdkit.py
@@ -7,7 +7,7 @@
 import pytest
 from rdkit import Chem
 
-from opencadd.io import Rdkit
+from opencadd.io.rdkit import Rdkit
 
 PATH_TEST_DATA = Path(__name__).parent / "opencadd" / "tests" / "data" / "io"