Merge pull request #5 from BiomedSciAI/add_downloads_and_clones_badges

Add downloads and clones badges

.github/workflows/clone.yml

@@ -0,0 +1,90 @@
+name: GitHub Clone Count Update Everyday
+
+on:
+  schedule:
+    - cron: "0 */24 * * *"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: gh login
+        run: echo "${{ secrets.SECRET_TOKEN }}" | gh auth login --with-token
+
+      - name: parse latest clone count
+        run: |
+          curl --user "${{ github.actor }}:${{ secrets.SECRET_TOKEN }}" \
+            -H "Accept: application/vnd.github.v3+json" \
+            https://api.github.com/repos/${{ github.repository }}/traffic/clones \
+            > clone.json
+
+      - name: create gist and download previous count
+        id: set_id
+        run: |
+          if gh secret list | grep -q "GIST_ID"
+          then
+              echo "GIST_ID found"
+              echo "GIST=${{ secrets.GIST_ID }}" >> $GITHUB_OUTPUT
+              curl https://gist.githubusercontent.com/${{ github.actor }}/${{ secrets.GIST_ID }}/raw/clone.json > clone_before.json
+              if cat clone_before.json | grep '404: Not Found'; then
+                echo "GIST_ID not valid anymore. Creating another gist..."
+                gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+                echo $gist_id | gh secret set GIST_ID
+                echo "GIST=$gist_id" >> $GITHUB_OUTPUT
+                cp clone.json clone_before.json
+                git rm --ignore-unmatch  CLONE.md
+              fi
+          else
+              echo "GIST_ID not found. Creating a gist..."
+              gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+              echo $gist_id | gh secret set GIST_ID
+              echo "GIST=$gist_id" >> $GITHUB_OUTPUT
+              cp clone.json clone_before.json
+          fi
+
+      - name: update clone.json
+        run: |
+          curl https://raw.githubusercontent.com/MShawon/github-clone-count-badge/master/main.py > main.py
+          python3 main.py
+
+      - name: Update gist with latest count
+        run: |
+          content=$(sed -e 's/\\/\\\\/g' -e 's/\t/\\t/g' -e 's/\"/\\"/g' -e 's/\r//g' "clone.json" | sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g')
+          echo '{"description": "${{ github.repository }} clone statistics", "files": {"clone.json": {"content": "'"$content"'"}}}' > post_clone.json
+          curl -s -X PATCH \
+            --user "${{ github.actor }}:${{ secrets.SECRET_TOKEN }}" \
+            -H "Content-Type: application/json" \
+            -d @post_clone.json https://api.github.com/gists/${{ steps.set_id.outputs.GIST }} > /dev/null 2>&1
+
+          if [ ! -f CLONE.md ]; then
+            shields="https://img.shields.io/badge/dynamic/json?color=success&label=Clone&query=count&url="
+            url="https://gist.githubusercontent.com/${{ github.actor }}/${{ steps.set_id.outputs.GIST }}/raw/clone.json"
+            repo="https://github.com/MShawon/github-clone-count-badge"
+            echo ''> CLONE.md
+            echo '
+            **Markdown**
+
+            ```markdown' >> CLONE.md
+            echo "[![GitHub Clones]($shields$url&logo=github)]($repo)" >> CLONE.md
+            echo '
+            ```
+
+            **HTML**
+            ```html' >> CLONE.md
+            echo "<a href='$repo'><img alt='GitHub Clones' src='$shields$url&logo=github'></a>" >> CLONE.md
+            echo '```' >> CLONE.md
+            
+            git add CLONE.md
+            git config --global user.name "GitHub Action"
+            git config --global user.email "[email protected]"
+            git commit -m "create clone count badge"
+          fi
+
+      - name: Push
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-publish.yml

@@ -0,0 +1,70 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# 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.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

CLONE.md

@@ -0,0 +1,13 @@
+
+
+  **Markdown**
+
+  ```markdown
+[![GitHub Clones](https://img.shields.io/badge/dynamic/json?color=success&label=Clone&query=count&url=https://gist.githubusercontent.com/mosheraboh/519a49d9073e04d2cc98dc7bb5805677/raw/clone.json&logo=github)](https://github.com/MShawon/github-clone-count-badge)
+
+  ```
+
+  **HTML**
+  ```html
+<a href='https://github.com/MShawon/github-clone-count-badge'><img alt='GitHub Clones' src='https://img.shields.io/badge/dynamic/json?color=success&label=Clone&query=count&url=https://gist.githubusercontent.com/mosheraboh/519a49d9073e04d2cc98dc7bb5805677/raw/clone.json&logo=github'></a>
+```

README.md

@@ -1,3 +1,7 @@
+[![PyPI Downloads](https://static.pepy.tech/badge/biomed-multi-view)](https://pepy.tech/projects/biomed-multi-view)
+[![GitHub Clones](https://img.shields.io/badge/dynamic/json?color=success&label=Clone&query=count&url=https://gist.githubusercontent.com/mosheraboh/519a49d9073e04d2cc98dc7bb5805677/raw/clone.json&logo=github)](https://github.com/MShawon/github-clone-count-badge)
+
+
 # Introduction
 
 This repository contains the implementation of the Multi-view Molecular Embedding with Late Fusion (MMELON) architecture presented in our preprint [Multi-view biomedical foundation models for molecule-target and property prediction](https://arxiv.org/abs/2410.19704). MMELON is a flexible approach to aggregate multiple views (sequence, image, graph) of molecules in a foundation model setting. While models based on single view representation typically performs well on some downstream tasks and not others, the multi-view model performs robustly across a wide range of property prediction tasks encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. It has been applied to screen compounds against a large (> 100 targets) set of G Protein-Coupled receptors (GPCRs) to identify strong binders for 33 targets related to Alzheimer’s disease, which are validated through structure-based modeling and identification of key binding motifs.