Merge branch 'a-r-j:master' into amorehead-pdbmanager-chain-interface…

…-filtering
amorehead · Sep 12, 2023 · ea2e2f3 · ea2e2f3
2 parents 6518dc7 + 6d5972f
commit ea2e2f3
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Showing 7 changed files with 25 additions and 9 deletions.
diff --git a/.requirements/base.in b/.requirements/base.in
@@ -1,5 +1,5 @@
 pandas<2.0.0
-biopandas==0.5.0.dev0
+biopandas>=0.5.0.dev0
 biopython
 bioservices>=1.10.0
 deepdiff

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,12 @@
-### 1.7.1 - UNRELEASED
+### 1.7.3 - 30/08/2023
+
+* Fixes edge case in FoldComp database download if target directory has same name as database ([#339](https://github.com/a-r-j/graphein/pull/339))
+
+### 1.7.2 - 28/08/2023
+
+* Pins BioPandas version to latest
+
+### 1.7.1 - 26/07/2023
 
 #### New Features
 * [Feature] - [#305](https://github.com/a-r-j/graphein/pull/305) Adds the `add_virtual_beta_carbon_vector` function inspired by [RFdiffusion](https://github.com/RosettaCommons/RFdiffusion/blob/main/rfdiffusion/coords6d.py#L37) and ProteinMPNN.
@@ -12,6 +20,9 @@
 * [Bugfix] - [#305](https://github.com/a-r-j/graphein/pull/305) Fixes the construction of geometric features when beta-carbons or side chains are missing in non-glycine residues (for example in `H:CYS:104` in 3SE8).
 * [Bugfix] - [#305](https://github.com/a-r-j/graphein/pull/305) Fixes data types of geometric feature vectors: `object` -> `float`.
 * [Bugfix] - [#301](https://github.com/a-r-j/graphein/pull/301) Fixes the conversion of undirected NetworkX graph to directed PyG data.
+* [Bugfix] - [#334](https://github.com/a-r-j/graphein/pull/334) Fixes the corner case of the NetworkX -> PyG conversion when input graph has no edges.
+
+https://github.com/a-r-j/graphein/pull/334
 
 #### Bugfixes
 * Adds missing `stage` parameter to `graphein.ml.datasets.foldcomp_data.FoldCompDataModule.setup()`. [#310](https://github.com/a-r-j/graphein/pull/310)
@@ -22,6 +33,7 @@
 * Fixes initialisation of `Protein` objects. [#317](https://github.com/a-r-j/graphein/issues/317) [#318](https://github.com/a-r-j/graphein/pull/318)
 * Fixes incorrect `rad` and `embed` argument logic in `graphein.protein.tensor.angles.dihedrals/sidechain_torsion` [#321](https://github.com/a-r-j/graphein/pull/321)
 * Fixes incorrect start padding in pNeRF output [#321](https://github.com/a-r-j/graphein/pull/321)
+* Fixes `pyyaml` breaking installation [#328](https://github.com/a-r-j/graphein/pull/328)
 * Fixes setting ID for PyG data objects when loading from a path to a `.pdb` file [#332](https://github.com/a-r-j/graphein/pull/332)
 
 #### Other Changes

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -34,7 +34,7 @@
 copyright = f"{datetime.datetime.now().year}, {author}"
 
 # The full version, including alpha/beta/rc tags
-release = "1.7.0"
+release = "1.7.3"
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/graphein/__init__.py b/graphein/__init__.py
@@ -12,7 +12,7 @@
 from .testing import *
 
 __author__ = "Arian Jamasb <arian@jamasb.io>"
-__version__ = "1.7.0"
+__version__ = "1.7.3"
 
 
 logger.configure(

diff --git a/graphein/ml/conversion.py b/graphein/ml/conversion.py
@@ -289,7 +289,8 @@ def convert_nx_to_pyg(self, G: nx.Graph) -> Data:
                     data[key].append(value)
 
         # Add edge features
-        edge_feature_names = list(G.edges(data=True))[0][2].keys()
+        edge_list = list(G.edges(data=True))
+        edge_feature_names = edge_list[0][2].keys() if edge_list else []
         edge_feature_names = list(
             filter(
                 lambda x: x in self.columns and x != "kind", edge_feature_names

diff --git a/graphein/ml/datasets/foldcomp_dataset.py b/graphein/ml/datasets/foldcomp_dataset.py
@@ -205,16 +205,19 @@ def download(self):
             os.path.exists(self.root / f) for f in self._database_files
         ):
             log.info(f"Downloading FoldComp dataset {self.database}...")
+            curr_dir = os.getcwd()
+            os.chdir(self.root)
             try:
                 foldcomp.setup(self.database)
             except RuntimeError:
                 _ = self.async_setup()
                 asyncio.run(_)
+            os.chdir(curr_dir)
             log.info("Download complete.")
-            log.info("Moving files to raw directory...")
+            # log.info("Moving files to raw directory...")
 
-            for f in self._database_files:
-                shutil.move(f, self.root)
+            # for f in self._database_files:
+            #    shutil.move(f, self.root)
         else:
             log.info(f"FoldComp database already downloaded: {self.root}.")
 

diff --git a/setup.py b/setup.py
@@ -134,7 +134,7 @@ def run(self):
 
 setup(
     name="graphein",
-    version="1.7.0",
+    version="1.7.3",
     description="Protein & Interactomic Graph Construction for Machine Learning",
     long_description=long_description,
     long_description_content_type="text/markdown",