rcsb-embedding-model 0.0.13__tar.gz → 0.0.15__tar.gz

rcsb_embedding_model-0.0.15/.github/workflows/_workflow-docker.yaml

@@ -0,0 +1,17 @@
+# Docker build and push workflow
+
+name: Run CI/CD Docker Workflow
+
+on:
+  workflow_call:
+
+jobs:
+  run-workflow:
+    if: github.event_name == 'release'
+    name: "Run automated docker workflow"
+    uses: rcsb/devops-cicd-github-actions/.github/workflows/workflow-docker.yaml@master
+    with:
+      dockerfile_location: "Dockerfile"  # The location of the Dockerfile relative to the root of the repository. Defaults to "Dockerfile".
+      repo_project: "rcsb"  # REQUIRED. The name of the project or organization in the remote Docker image repository.
+      docker_image_name: "rcsb-embedding-model"  # REQUIRED. The name of the Docker image to create.
+      docker_build_context: "."  # The path location of the docker build context, relative to the project root. Defaults to the project root.

rcsb_embedding_model-0.0.15/.github/workflows/publish.yaml

@@ -0,0 +1,94 @@
+name: CI Pipeline
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+
+jobs:
+  hatch-test:
+    name: Test on Python ${{ matrix.python-version }}
+    runs-on: ["self-hosted", "buildchain"]
+    timeout-minutes: 20
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential pkg-config libzstd-dev
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Hatch and HaggingFace
+        run: pip install hatch huggingface_hub[cli]
+
+      - name: Authenticate to Hugging Face
+        run: huggingface-cli login --token ${{ secrets.HF_API_TOKEN }}
+
+      - name: Run tests
+        run: hatch test
+
+  hatch-build:
+    name: Build to PyPI
+    needs: hatch-test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Hatch
+        run: pip install hatch
+
+      - name: Build distribution
+        run: hatch build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: github.event_name == 'release'
+    needs:
+      - hatch-build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/rcsb-embedding-model
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  push-image:
+    needs:
+      - hatch-test
+    name: Push image to harbor
+    uses: ./.github/workflows/_workflow-docker.yaml

rcsb_embedding_model-0.0.15/Dockerfile

@@ -0,0 +1,6 @@
+FROM python:3.10
+
+WORKDIR /app
+COPY . /app/
+
+RUN pip install --no-cache-dir -e .

{rcsb_embedding_model-0.0.13 → rcsb_embedding_model-0.0.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.13
+Version: 0.0.15
 Summary: Protein Embedding Model for Structure Search
 Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
 Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
@@ -18,7 +18,7 @@ Description-Content-Type: text/markdown
 
 # RCSB Embedding Model
 
-**Version** 0.0.13
+**Version** 0.0.15
 
 
 ## Overview

{rcsb_embedding_model-0.0.13 → rcsb_embedding_model-0.0.15}/README.md

@@ -1,6 +1,6 @@
 # RCSB Embedding Model
 
-**Version** 0.0.13
+**Version** 0.0.15
 
 
 ## Overview

{rcsb_embedding_model-0.0.13 → rcsb_embedding_model-0.0.15}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rcsb-embedding-model"
-version = "0.0.13"
+version = "0.0.15"
 authors = [
     { name="Joan Segura", email="joan.segura@rcsb.org" },
 ]

{rcsb_embedding_model-0.0.13 → rcsb_embedding_model-0.0.15}/tests/test_remote_inference.py

@@ -14,8 +14,8 @@ class TestRemoteInference(unittest.TestCase):
 
         esm_embeddings = predict(
             src_stream=[
-                ("3jce", "https://files.rcsb.org/download/3jce.cif", "3jce"),
-                ("9qxy", "https://files.rcsb.org/download/9qxy.cif", "9qxy")
+                ("1acb", "https://files.rcsb.org/download/1acb.cif", "1acb"),
+                ("2uzi", "https://files.rcsb.org/download/2uzi.cif", "2uzi")
             ],
             src_location=SrcLocation.stream,
             src_from=SrcProteinFrom.structure,
@@ -24,8 +24,8 @@ class TestRemoteInference(unittest.TestCase):
             accelerator=Accelerator.cpu
         )
 
-        self.assertEqual(len(esm_embeddings), 52)
-        shapes = ((208, 1536), (207, 1536), (152, 1536), (104, 1536), (153, 1536), (131, 1536), (129, 1536), (100, 1536), (119, 1536), (125, 1536), (116, 1536), (102, 1536), (90, 1536), (84, 1536), (82, 1536), (57, 1536), (81, 1536), (87, 1536), (53, 1536), (220, 1536), (58, 1536), (52, 1536), (48, 1536), (66, 1536), (40, 1536), (236, 1536), (272, 1536), (211, 1536), (203, 1536), (179, 1536), (178, 1536), (151, 1536), (143, 1536), (144, 1536), (124, 1536), (145, 1536), (138, 1536), (122, 1536), (118, 1536), (116, 1536), (119, 1536), (105, 1536), (112, 1536), (95, 1536), (104, 1536), (96, 1536), (81, 1536), (79, 1536), (65, 1536), (60, 1536), (588, 1536), (208, 1536))
+        self.assertEqual(len(esm_embeddings), 5)
+        shapes = ((243, 1536), (65, 1536), (116, 1536), (106, 1536), (168, 1536))
         for idx, shape in enumerate(shapes):
             self.assertEqual(tuple(esm_embeddings[idx][0][0].shape), shape)
 

rcsb_embedding_model-0.0.13/tests/resources/esm-from-chain-inference.csv

@@ -1,2 +0,0 @@
-8GYM,/Users/joan/tmp/8GYM.cif,A,8GYM.A
-2YBB,/Users/joan/tmp/2YBB.cif,A,2YBB.A