Merge branch 'alignments' of https://github.com/PyEED/pyeed into alig…

…nments

.github/workflows/Dockerfile

@@ -0,0 +1,21 @@
+# jupyter/scipy-notebook to build our image on top of it
+FROM jupyter/scipy-notebook
+
+LABEL Max Haeussler <[email protected]>
+
+USER root
+
+# Install psycopg2 dependencies
+RUN apt-get update \
+    && apt-get -y install libpq-dev gcc python3-dev\
+    && pip install psycopg2
+
+# Install python libraries
+RUN pip install --upgrade pip \
+    && pip install git+https://github.com/PyEED/pyeed.git@alignments
+
+# Let's change to  "$NB_USER" command so the image runs as a non root user by default
+USER $NB_UID
+
+#Let's define this parameter to install jupyter lab instead of the default juyter notebook command so we don't have to use it when running the container with the option -e
+ENV JUPYTER_ENABLE_LAB=yes

.github/workflows/build_push_docker.yaml

@@ -0,0 +1,37 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image
+on:
+  push:
+    branches:
+      - "alignments"
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: haeussma/pyeed-notebook:latest

pyEED/alignment/pairwise.py

@@ -69,7 +69,7 @@ def pairwise_alignment(
         FileNotFoundError: If the substitution matrix is not valid.
 
     Returns:
-        PairwiseAlignment: Pairwise alignment object with the alignment scores.
+        Alignment: Pairwise alignment object with the alignment scores.
     """
     modes = ["global", "local"]
 

pyEED/network/network.py

@@ -3,23 +3,23 @@
 import plotly.graph_objects as go
 
 from pyEED.core.proteininfo import ProteinInfo
-from pyEED.core.pairwisealignment import PairwiseAlignment
+from pyEED.core.alignment import Alignment
 
 
 def pairwise_network(
-    alignments: List[PairwiseAlignment],
+    alignments: List[Alignment],
     weight: str = "identity",
     cutoff: float = None,
     label: str = "accession_id",
     color: str = "name",
 ) -> None:
-    """Takes a list of `PairwiseAlignment`, constructs a network graph,
+    """Takes a list of `Alignment`, constructs a network graph,
     whereas the edges of the graph are weighted with an attribute of the
-    `PairwiseAlignment` object. Visualizes the network graph.
+    `Alignment` object. Visualizes the network graph.
 
     Args:
-        alignments (List[PairwiseAlignment]): List of pairwise alignments.
-        weight (str, optional): Attribute of `PairwiseAlignment` to weight the edges.
+        alignments (List[Alignment]): List of pairwise alignments.
+        weight (str, optional): Attribute of `Alignment` to weight the edges.
         Defaults to "identity".
         cutoff (float, optional): Sequences with a weight higher than the cutoff are connected
         in the network. Defaults to None.
@@ -53,7 +53,7 @@ def pairwise_network(
     visualize_network(graph, label=label, color=color)
 
 
-def construct_network(alignments: List[PairwiseAlignment], cutoff: float) -> nx.Graph:
+def construct_network(alignments: List[Alignment], cutoff: float) -> nx.Graph:
     """Maps properties of alignments to a network graph."""
     graph = nx.Graph()
 
@@ -187,7 +187,7 @@ def position_nodes_and_edges(graph: nx.Graph, weight: str) -> nx.Graph:
     return graph
 
 
-def _get_unique_sequences(alignments: List[PairwiseAlignment]) -> List[ProteinInfo]:
+def _get_unique_sequences(alignments: List[Alignment]) -> List[ProteinInfo]:
     """Gets unique sequences from a list of alignments."""
 
     sequence_infos = []

pyproject.toml

@@ -8,7 +8,8 @@ readme = "README.md"
 packages = [
     { include = "pyEED/core" },
     { include = "pyEED/ncbi" },
-    { include = "pyEED/networks" },
+    { include = "pyEED/network" },
+    { include = "pyEED/alignment" },
 ]
 
 [tool.poetry.dependencies]