Added ModelAngelo to cmake and added weights download attempt during …

…cmake configure time.

CMakeLists.txt

@@ -454,6 +454,8 @@ list(APPEND RELION_PYTHON_WRAPPERS
         python_blush
         python_dynamight
         python_topaz
+        python_modelangelo
+        python_fetch_weights
 	python_tomo_import
 	python_tomo_exclude_tilt_images
 	python_tomo_align_tilt_series
@@ -472,6 +474,21 @@ foreach (SCRIPT_FILE ${RELION_PYTHON_WRAPPERS})
     )
 endforeach()
 
+message(STATUS "Will attempts to download model weights for dependent packages...")
+
+execute_process(
+        COMMAND bash ${CMAKE_BINARY_DIR}/bin/relion_python_fetch_weights
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        RESULT_VARIABLE SCRIPT_RESULT
+)
+
+# Check the result of the script execution
+if(SCRIPT_RESULT EQUAL 0)
+    message(STATUS "Successfully downloaded model weights")
+else()
+    message(WARNING "Failed to download model weights: ${SCRIPT_RESULT}")
+endif()
+
 # ----------------------------------------------------------------------COPY SCRIPTS--
 
 if(FORCE_OWN_FFTW)

environment.yml

@@ -25,10 +25,15 @@ dependencies:
       - fastcluster==1.2.6
       - seaborn==0.12.2
       - dill==0.3.7
+      - pyhmmer>=0.10.1
+      - fair-esm
+      - einops
+      - scipy
       - git+https://github.com/3dem/relion-classranker@b6e751e5cb4205d8e9b36d0ae38c3687b3395acb
       - git+https://github.com/3dem/relion-blush
       - git+https://github.com/3dem/DynaMight
       - git+https://github.com/3dem/topaz
+      - git+https://github.com/3dem/model-angelo
       - ".[vis]"
 
 

scripts/python_fetch_weights.in

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+# Get the directory of the currently executing script
+script_dir="$(dirname "$0")"
+
+# Call Class Ranker weight download ##############################################
+echo "Attempting to download weights for class ranker..."
+
+target_path="$script_dir/relion_python_classranker"
+
+if [ -x "$target_path" ]; then
+  # Execute the target binary
+  "$target_path"
+else
+  echo "Error: $target_binary not found or not executable in $script_dir."
+  exit 1
+fi
+
+# Call Blush weight download #####################################################
+echo "Attempting to download weights for Blush..."
+
+target_path="$script_dir/relion_python_blush"
+
+if [ -x "$target_path" ]; then
+  # Execute the target binary
+  "$target_path"
+else
+  echo "Error: $target_binary not found or not executable in $script_dir."
+  exit 1
+fi
+
+# ModelAngelo weight download ####################################################
+echo "Attempting to download weights for ModelAngelo..."
+target_path="$script_dir/relion_python_modelangelo"
+
+if [ -x "$target_path" ]; then
+  # Execute the target binary
+  "$target_path"
+else
+  echo "Error: $target_binary not found or not executable in $script_dir."
+  exit 1
+fi
+
+# Exit
+exit 0
+

scripts/python_modelangelo.in

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+print_error() {
+echo "
+---------------------------------- PYTHON ERROR ---------------------------------
+   Has RELION been provided a Python interpreter with the correct environment?
+   The interpreter can be passed to RELION either during Cmake configuration by
+     using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.
+   NOTE: For some modules TORCH_HOME needs to be set to find pretrained models
+---------------------------------------------------------------------------------
+
+  Using python executable: $1
+"
+}
+
+# Set the Python executable path
+python_executable="@PYTHON_EXE_PATH@"
+torch_home="@TORCH_HOME_PATH@"
+
+# Check if the python executable exists
+if [ ! -x "$python_executable" ]; then
+    # Check for default python executable
+    python_executable=$(command -v python)
+
+    if [ -z "$python_executable" ]; then
+        print_error "$python_executable"
+        exit 1
+    fi
+fi
+
+# Run the Python script with forwarded arguments
+if [ -n "$torch_home" ]; then
+  TORCH_HOME="$torch_home" "$python_executable" -c "from model_angelo.__main__ import main; exit(main())" "$@"
+else
+  "$python_executable" -c "from model_angelo.__main__ import main; exit(main())" "$@"
+fi
+
+# Check the return status of the python command
+if [ $? -ne 0 ]; then
+    print_error "$python_executable"
+    exit 2
+fi
+
+# Exit
+exit 0
+