Use of dynamic dependencies (#905)

## Note: This PR needs to be merged after
[xmipp-995](I2PC/xmipp3#995).
- `xmipp3-installer` will now be automatically installed with the plugin
to ease Xmipp's new installation process.
- Instead of pointing to a specific Xmipp's version (`v3.24.0`, for
example), a new dynamic tag `v3` is used, to avoid needing to release a
new version of the plugin just because a new release of xmipp was
generated. Now releases in the plugin will only be tiggered by changes
in the code of the plugin itself, nothing else.

---------

Co-authored-by: Oier Lauzirika Zarrabeitia <[email protected]>
Co-authored-by: alberto <[email protected]>

Author: 3 people

.github/workflows/build.yml

@@ -2,15 +2,11 @@ name: Build plugin
 
 on:
   pull_request:
-    branches: [devel, master]
+  workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-22.04
-    
-    # Avoid send statistics
-    env:
-      SEND_INSTALLATION_STATISTICS: OFF
 
     steps:    
     - name: Checkout repository
@@ -23,14 +19,6 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y libfftw3-dev libopenmpi-dev libhdf5-dev libtiff5-dev libsqlite3-dev default-jdk git cmake openmpi-bin gcc g++
 
-    - name: Install CUDA
-      uses: Jimver/cuda-toolkit@master
-      id: cuda-toolkit
-      with:
-        cuda: '11.8.0'
-        method: network
-        sub-packages: '["nvcc", "toolkit"]'
-
     - name: Install Miniconda
       uses: conda-incubator/setup-miniconda@main
       with:
@@ -39,41 +27,26 @@ jobs:
         auto-activate-base: true
         activate-environment: scipion3
         python-version: "3.8"
-        
+
     - name: Install Scipion
-      working-directory: ${{ github.workspace }}
+      working-directory: ${{ github.workspace }}/../
       run: |
-        pwd
         pip install --user scipion-installer
         python -m scipioninstaller -conda -noAsk scipion
 
-        
-    - name: Cloning scipion-em-xmipp
-      working-directory: ${{ github.workspace }}/scipion/
+    - name: Install xmipp3-installer
+      working-directory: ${{ github.workspace }}
       run: |
-           pwd
-           rm -rf scipion-em-xmipp
-           git clone https://github.com/I2PC/scipion-em-xmipp.git
+        pip install --user xmipp3-installer
 
-    - name: Conditionally checkout to ${{ github.head_ref }}
-      working-directory: ${{ github.workspace }}/scipion/scipion-em-xmipp
-      env:
-        BRANCH_NAME: ${{ github.head_ref }}
-      run: |
-          pwd
-          git checkout $BRANCH_NAME
-   
-    - name: Install and compile Xmipp and show log
-      working-directory: ${{ github.workspace }}/scipion/ 
-      env:
-        BUILD_TESTS: True
-        BRANCH_NAME: ${{ github.head_ref }}
-        SEND_INSTALLATION_STATISTICS: OFF 
+    - name: Cloning xmipp and getting sources
+      working-directory: ${{ github.workspace }}/../
       run: |
-          pwd
-          ./scipion3 installp -p scipion-em-xmipp --devel || {
-          echo "First attempt failed. Retrying..."
-          sleep 10
-          ./scipion3 installp -p scipion-em-xmipp --devel || (cat compilation.log && false)
-          }
-      # Duplicated because a defineVariables scipion plugin fails
+        git clone https://github.com/I2PC/xmipp3.git
+        ./xmipp3/xmipp getSources --keep-output
+        cd xmipp3/src/
+        ln -s "${{ github.workspace }}" "${{ github.workspace }}/../xmipp3/src/scipion-em-xmipp"
+
+    - name: Installing scipion-em-xmipp
+      working-directory: ${{ github.workspace}}/../xmipp3/src
+      run: ../../scipion/scipion3 installp -p scipion-em-xmipp/ --devel

.github/workflows/release.yml

@@ -1,11 +1,14 @@
 name: Release
 on:
-  push:
-    branches: [ master ]
+  workflow_dispatch:
 
 jobs:
   release:
+    environment:
+      name: release-approval
+
     runs-on: ubuntu-latest
+
     steps:
     - name: Checkout
       uses: actions/checkout@main
@@ -17,37 +20,43 @@ jobs:
       uses: actions/setup-python@main
       with:
         python-version: '3.8'
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine build
         pip install -r requirements.txt
-      
+
+    - name: Switch xmipp from devel to release
+      run: |
+        sed -i -E "s/^(type_of_version[[:space:]]*=[[:space:]]*)'devel'/\1'release'/" xmipp3/version.py
+        git add xmipp3/version.py
+        git config --global user.name "github-actions"
+        git config --global user.email "[email protected]"
+        git commit -m "Switch xmipp from devel to release"
+
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python -m build --no-isolation
         twine upload dist/* -c "${{ secrets.PYPI_COMMENT }}"
-  
+
     - name: Get changelog, tag name, & release name
       id: variables
-      run: |
-        awk '/## Release/{if (p) exit; p=1} p' CHANGELOG.md > latest_changelog_with_title.md
-        cat latest_changelog_with_title.md | tail -n +2 > latest_changelog.md
-        RELEASE_NAME=$(cat latest_changelog_with_title.md | head -n 1 | sed 's/## Release //' | sed 's/^ *//')
-        echo "RELEASE_NAME=$RELEASE_NAME" >> $GITHUB_OUTPUT
-        echo "TAG_NAME=${RELEASE_NAME// /}" >> $GITHUB_OUTPUT
-    
+      run:
+        TAG_NAME=$(grep "_pluginVersion" xmipp3/version.py | sed -E 's/.*"([^"]+)".*/\1/')
+        RELEASE_NAME="Release ${TAG_NAME}"
+        echo "TAG_NAME=$TAG_NAME" >> $GITHUB_OUTPUT
+
     - name: Generate tag
       id: tag_version
       uses: mathieudutour/[email protected]
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         custom_tag: ${{ steps.variables.outputs.TAG_NAME }}
-    
+
     - name: Create a GitHub release
       uses: ncipollo/release-action@main
       with:

requirements.txt

@@ -8,4 +8,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
-
+xmipp3-installer==2.*
+numpy==1.*

xmipp3/__init__.py

@@ -45,8 +45,6 @@
 
 type_of_version = version.type_of_version
 _logo = version._logo
-_binTagVersion = version._binTagVersion
-_pluginTagVersion= version._pluginTagVersion
 _currentDepVersion = version._currentDepVersion
 __version__ = version.__version__
 
@@ -199,16 +197,15 @@ def defineBinaries(cls, env):
 	            default=False
 	        )
         else:
-            xmippSrc = f'xmippSrc-{version._binTagVersion}'
+            xmippSrc = f'xmipp3-{version._binVersion}'
             installCommands = [
                 (f'cd .. && rm -rf {xmippSrc} && '
-                f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+                f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
                 f'cd {xmippSrc} && '
-                f'git checkout {version._binTagVersion} && '
                 f'./xmipp --production True ', COMPILE_TARGETS)
             ]
             env.addPackage(
-	                'xmippSrc', version=version._binTagVersion,
+	                'xmipp3', version=version._binVersion,
 	                tar='void.tgz',
 	                commands=installCommands,
 	                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
@@ -228,7 +225,7 @@ def __getBundleDirectory(cls):
 
         isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
-        
+        print(f'pluginDir: {pluginDir}\n, bundleDir: {bundleDir}\n, isBundle: {isBundle}')
         return bundleDir if isBundle else None
 
 def getNvidiaDriverVersion(plugin):

xmipp3/constants.py

@@ -28,7 +28,7 @@
 """
 
 # ------------------ Constants values --------------------------------------
-XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp.git'
+XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp3.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
 NMA_HOME = 'NMA_HOME'

xmipp3/version.py

@@ -28,11 +28,18 @@
 type_of_version = 'devel' #'release' 'devel'
 _logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
 
-_binVersion = 'v3.25.06.0' # Increase it if hotfix in binaries (xmipp, xmippCore and/or XmippViz)
-_pluginVersion = 'v3.25.06.0' # Increase it if hotfix in binaries (xmipp, xmippCore and/or XmippViz) or in scipion-em-xmipp
-
-_binTagVersion = _binVersion + '-Rhea' #'devel' or _binVersion + '-Poseidon'
-_pluginTagVersion = _pluginVersion + '-Rhea'  #'devel' or _pluginVersion + '-Poseidon'
+_binVersion = 'v4' # Increase it if major release is generated in xmipp
+# Increase according to SemVer rules:
+# Rules with initial package version of vX.Y.Z
+# - If the change consists of fixing a bug (that does not change at all
+#   how the protocols are used), increase Z by 1.
+# - If the change is adding new functionality (extra params for a protocol,
+#   or new protocols), increase Y by 1.
+# - If the change deprecates existing functionality (remove a protocol,
+#   or a param), increase X by 1
+# - If several of the above are true, only change the biggest one applicable (
+#   for example, if a fix is made and a new protocol are included in the same
+#   pull request, increase the one related to the new protocol).
+__version__ = 'v4.0.0'
 
 _currentDepVersion = '1.0'
-__version__ = _pluginVersion[3:] # Name of the pypi package