Added release actions

.github/workflows/build.yml

@@ -0,0 +1,61 @@
+name: Build plugin on Pull Request
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Free Disk Space (Ubuntu only)
+      uses: jlumbroso/free-disk-space@main
+
+    - name: Set up MPI
+      uses: mpi4py/setup-mpi@master
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y wget gcc-10 g++-10 make
+
+    - name: Install Miniconda
+      uses: conda-incubator/setup-miniconda@main
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        auto-activate-base: true
+        activate-environment: scipion3
+        python-version: "3.8"
+
+    - name: Install Scipion
+      working-directory: ${{ github.workspace }}/../
+      run: |
+        pip cache purge
+        pip install --user scipion-installer
+        python3 -m scipioninstaller -conda -noXmipp -noAsk scipion
+
+    # Installing scipion-chem
+    # Checkout to Pull Request branch if exists, by default stays in devel
+    - name: Install scipion-chem (in branch ${{ github.head_ref }} if exists)
+      working-directory: ${{ github.workspace }}/../
+      env:
+        REPO_NAME: scipion-chem
+        BRANCH_NAME: ${{ github.head_ref }}
+      run: |
+        git clone https://github.com/scipion-chem/$REPO_NAME.git
+        if [ $(git ls-remote --heads https://github.com/scipion-chem/$REPO_NAME.git $BRANCH_NAME | wc -l) -eq 1 ]; then
+          cd $REPO_NAME && git checkout $BRANCH_NAME && cd -
+        fi
+        scipion/scipion3 installp -p $REPO_NAME --devel
+
+    - name: Checkout repository
+      uses: actions/checkout@main
+      with:
+        ref: ${{ github.head_ref }}
+
+    - name: Install plugin from pull request
+      working-directory: ${{ github.workspace }}
+      run: |
+        pip cache purge
+        ../scipion/scipion3 installp -p . --devel

.github/workflows/release.yml

@@ -0,0 +1,53 @@
+name: Generate release (Pypi, tag, & GitHub Release)
+on: workflow_dispatch
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@main
+
+    - name: Set up MPI
+      uses: mpi4py/setup-mpi@master
+
+    - name: Set up Python
+      uses: actions/setup-python@main
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        pip install setuptools wheel twine
+        pip install -r requirements.txt
+
+    - name: Get tag name
+      id: variables
+      env:
+        FOLDER_WITH_VERSION: ${{ vars.FOLDER_WITH_VERSION }}
+      run: |
+        VERSION=$(python -c "import $FOLDER_WITH_VERSION; print('VERSION', 'v'+$FOLDER_WITH_VERSION.__version__)" | grep VERSION | sed "s/VERSION //g") || (echo "Could not import version, check that variables are correctly set!" && exit 1)
+        echo "TAG_NAME=${VERSION#v}" >> $GITHUB_OUTPUT
+        echo "TAG NAME (must not contain version prefix): ${VERSION#v}"
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist
+        twine upload dist/* -c "${{ secrets.PYPI_COMMENT }}"
+
+    - name: Generate tag
+      id: tag_version
+      uses: mathieudutour/github-tag-action@v6.2
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        custom_tag: ${{ steps.variables.outputs.TAG_NAME }}
+
+    - name: Create a GitHub release
+      uses: ncipollo/release-action@main
+      with:
+        tag: ${{ steps.tag_version.outputs.new_tag }}
+        name: ${{ steps.variables.outputs.TAG_NAME }}

protox/__init__.py

@@ -69,6 +69,3 @@ def getPluginH(cls, path=""):
 	@classmethod
 	def getScriptsPath(cls):
 		return cls.getPluginH('scripts/')
-
-
-

protox/constants.py

@@ -28,5 +28,3 @@
 # Version constants
 V1_0 = '1.0'
 PLUGIN_VERSION = '0.1'
-
-# Package dictionaries

protox/protocols/protocol_protox.py

@@ -4,7 +4,6 @@
 import os
 from urllib.request import urlopen
 
-
 # Specific imports
 from pyworkflow.protocol.params import PointerParam, EnumParam
 from pwem.protocols import EMProtocol
@@ -15,7 +14,6 @@
 import pandas as pd
 from pwchem.constants import RDKIT_DIC
 
-
 class ProtChemProtox(EMProtocol):
 
     """Toxicity prediction of small ligands with Protox"""
@@ -157,16 +155,3 @@ def getMainNameFromCID(self,cid):
             main_name = None
 
         return main_name
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protox/viewers/viewers_protox.py

@@ -72,5 +72,3 @@ def save_html_file(self, html_content):
             f.write(html_content)
 
         webbrowser.open('file://' + os.path.realpath(html_path))
-
-

requirements.txt

@@ -1,4 +1,3 @@
 scipion-pyworkflow
 scipion-em
 scipion-chem
-