Workflow fixes, documentation reorganization, and LibTorch integration

.claude/settings.local.json

@@ -0,0 +1,14 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(find:*)",
+      "Bash(git branch:*)",
+      "Bash(git show-branch:*)",
+      "Bash(git merge-base:*)",
+      "Bash(git ls-tree:*)",
+      "Bash(grep:*)"
+    ],
+    "deny": [],
+    "ask": []
+  }
+}

.github/workflows/check_formatting.yml

@@ -0,0 +1,52 @@
+name: Check C++ Formatting
+
+on:
+  push:
+    branches:
+      - master
+      - '*_with_ci'
+  pull_request:
+    branches: master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Check C++ formatting
+        uses: RafikFarhad/clang-format-github-action@v3
+        with:
+          sources: "src/**/*.cpp,src/**/*.h,src/**/*.cc,src/**/*.cxx,src/**/*.hpp,src/**/*.cu,src/**/*.cuh"
+          excludes: "include/**/*,src/gui/wxformbuilder/**/*,src/gui/*ProjectX_gui*"
+          style: file
+
+  # Build workflows - only run if formatting check passes
+  build-gpu-debug:
+    needs: check-format
+    uses: ./.github/workflows/debug_build.yml
+
+  build-cpu-debug:
+    needs: check-format
+    uses: ./.github/workflows/debug_build_cpu_only.yml
+
+  build-gpu-release:
+    needs: check-format
+    uses: ./.github/workflows/release_build.yml
+
+  build-gpu-release-gnu-mkl:
+    needs: check-format
+    uses: ./.github/workflows/release_build_GNU_mkl.yml
+
+  build-gpu-release-clang-mkl:
+    needs: check-format
+    uses: ./.github/workflows/release_build_clang_mkl.yml
+
+  build-gpu-release-no-experimental:
+    needs: check-format
+    uses: ./.github/workflows/release_build_full_no_experimental.yml

.github/workflows/debug_build.yml

@@ -1,15 +1,10 @@
 name: cisTEM GPU debug
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
-  run_build:  
+  run_build:
     uses: ./.github/workflows/run_builds.yml
     with:
       build_type: "GPU_debug"

.github/workflows/debug_build_cpu_only.yml

@@ -1,15 +1,10 @@
 name: cisTEM cpu debug
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
-  run_build:  
+  run_build:
     uses: ./.github/workflows/run_builds.yml
     with:
       build_type: "cpu_debug"

.github/workflows/release_build.yml

@@ -1,12 +1,7 @@
 name: cisTEM GPU release
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
   run_build:

.github/workflows/release_build_GNU_mkl.yml

@@ -1,12 +1,7 @@
 name: cisTEM GPU release, GNU MKL
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
   run_build:

.github/workflows/release_build_clang_mkl.yml

@@ -1,12 +1,7 @@
 name: cisTEM GPU release, clang MKL
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
   run_build:

.github/workflows/release_build_full_no_experimental.yml

@@ -1,12 +1,7 @@
 name: cisTEM GPU release no experimental full build
 
 on:
-  push:
-    branches: 
-      - master
-      - '*_with_ci'
-  pull_request:
-    branches: master
+  workflow_call:
 
 jobs:
   run_build:

.github/workflows/run_builds.yml

@@ -47,7 +47,7 @@ jobs:
       fail-fast: true
     runs-on: ${{ inputs.runs_on_os }}
     container: 
-      image: cistemdashorg/cistem_build_env:v2.2.1
+      image: cistemdashorg/cistem_build_env:v2.2.2
       options: --user root --rm
       # options: --user root --rm --gpus all
     outputs:

.gitignore

@@ -1,5 +1,9 @@
 autom4te.cache
-m4
+m4/*
+!m4/ax_cuda.m4
+!m4/additional_programs.m4
+!m4/submodule_FastFFT.m4
+!m4/libtorch.m4
 config.sub
 Makefile.in
 ltmain.sh
@@ -33,4 +37,7 @@ configure~
 *.tif
 *.dff
 __pycache__/
-include/Eigen
+include/Eigen
+
+.claude/cache/
+worktrees/

.vscode_shared/BenHimes/workspace.code-workspace

@@ -1,3 +1,4 @@
+
 {
     "folders": [
         {

.vscode_shared/CistemDev/CONTAINER_VERSION_BASE

@@ -1 +1 @@
-2.1.3
+2.2.0

.vscode_shared/CistemDev/CONTAINER_VERSION_TOP

@@ -1 +1 @@
-2.2.1
+2.2.2

.vscode_shared/CistemDev/devcontainer.json

@@ -1,6 +1,6 @@
 {
     "name": "cisTEMdev-wxSTABLE-static12",
-    "image": "cistemdashorg/cistem_build_env:v2.2.1",
+    "image": "cistemdashorg/cistem_build_env:v2.2.2",
     "remoteUser": "cisTEMdev",
     "hostRequirements": {
         "gpu": "optional"

.vscode_shared/CistemDev/settings.json

@@ -110,10 +110,11 @@
     "DockerRun.DisableDockerrc": true,
     "html.format.endWithNewline": true,
     "editor.fontSize": 12,
+    "editor.inlineSuggest.minShowDelay": 2,
     "remote.extensionKind": {
         "github.copilot-chat": "ui"
     },
-        "github.copilot.enable": {
+    "github.copilot.enable": {
         "*": true,
         "markdown": true,
         "scminput": false,
@@ -126,6 +127,28 @@
         "log": false,
         "matlab": true
     },
+    "chat.tools.terminal.autoApprove": {
+        "mkdir": true,
+        "echo": true,
+        "/^git (status|show|log)\\b/": true,
+        "ls": true,
+        "cd": true,
+        "pwd": true,
+        "cat": true,
+        "grep": true,
+        "head": true,
+        "tail": true,
+        "find": true,
+        "date": true,
+        "whoami": true,
+        "df": true,
+        "du": true,
+        "cp": false,
+        "mv": false,
+        "rm": false,
+        "del": false,
+        "/dangerous/": false
+    },
     "github.copilot.chat.codeGeneration.instructions": [],
     "github.copilot.chat.codeGeneration.useInstructionFiles": false
 }

.vscode_shared/CistemDev/tasks.json

@@ -6,7 +6,8 @@
         "env": {
             "cuda_dir": "/usr/local/cuda",
             "build_dir": "${workspaceFolder}/build",
-            "common_flags": " --enable-experimental --enable-openmp --disable-build-all --enable-profiling",
+            // -diag-file-append makes Intel compiler show absolute paths in error messages for easier IDE navigation
+            "common_flags": "--enable-experimental --enable-openmp --disable-build-all --enable-profiling",
             "experimental_algo_flags": "--enable-fp16-particlestacks  --disable-multiple-global-refinements",
             "common_optional_programs": "--enable-build-scale-with-mask --enable-build-create-mask --enable-build-resample --enable-build-resize"
             // "common_optional_programs": "--enable-build-sharpen-map --enable-build-convert-binary-to-star --enable-build-convert-eer-to-mrc --enable-build-resize --enable-build-resample --enable-build-sum_all_mrc_files --enable-build-sum_all_tif_files --enable-build-convert_par_to_star --enable-build-quick_test"
@@ -21,7 +22,19 @@
         {
             "label": "BUILD cisTEM",
             "type": "shell",
-            "command": "cd ${build_dir}/intel-gpu-static && make -j${input:compile_cores}"
+            "command": "cd ${build_dir}/intel-gpu-static && make -j${input:compile_cores} 2>&1 | sed -u 's|../../../src/|${workspaceFolder}/src/|g'",
+            "problemMatcher": {
+                "owner": "icpc",
+                "fileLocation": "absolute",
+                "pattern": {
+                    "regexp": "^(.*)\\((\\d+)\\):\\s+(warning|error|remark)\\s+#?(\\d+)?:\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "code": 4,
+                    "message": 5
+                }
+            }
         },
         {
             "label": "Configure cisTEM DEBUG build",
@@ -31,8 +44,20 @@
         {
             "label": "BUILD cisTEM DEBUG",
             "type": "shell",
-            "command": "cd ${build_dir}/intel-gpu-debug-static && make -j${input:compile_cores}"
-        }
+            "command": "cd ${build_dir}/intel-gpu-debug-static && make -j${input:compile_cores} 2>&1 | sed -u 's|../../../src/|${workspaceFolder}/src/|g'",
+            "problemMatcher": {
+                "owner": "icpc",
+                "fileLocation": "absolute",
+                "pattern": {
+                    "regexp": "^(.*)\\((\\d+)\\):\\s+(warning|error|remark)\\s+#?(\\d+)?:\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "code": 4,
+                    "message": 5
+                }
+            }
+        },
         {
             "label": "Configure cisTEM DEBUG build TMPVALUE",
             "type": "shell",
@@ -41,8 +66,20 @@
         {
             "label": "BUILD cisTEM DEBUG TMPVALUE",
             "type": "shell",
-            "command": "cd ${build_dir}/intel-gpu-debug-static-tmpvalue && make -j${input:compile_cores}"
-        }
+            "command": "cd ${build_dir}/intel-gpu-debug-static-tmpvalue && make -j${input:compile_cores} 2>&1 | sed -u 's|../../../src/|${workspaceFolder}/src/|g'",
+            "problemMatcher": {
+                "owner": "icpc",
+                "fileLocation": "absolute",
+                "pattern": {
+                    "regexp": "^(.*)\\((\\d+)\\):\\s+(warning|error|remark)\\s+#?(\\d+)?:\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "code": 4,
+                    "message": 5
+                }
+            }
+        },
         {
             "label": "Configure cisTEM DEBUG build, CPU only",
             "type": "shell",
@@ -51,7 +88,41 @@
         {
             "label": "BUILD cisTEM DEBUG, CPU only",
             "type": "shell",
-            "command": "cd ${build_dir}/intel-debug-static && make -j${input:compile_cores}"
+            "command": "cd ${build_dir}/intel-debug-static && make -j${input:compile_cores} 2>&1 | sed -u 's|../../../src/|${workspaceFolder}/src/|g'",
+            "problemMatcher": {
+                "owner": "icpc",
+                "fileLocation": "absolute",
+                "pattern": {
+                    "regexp": "^(.*)\\((\\d+)\\):\\s+(warning|error|remark)\\s+#?(\\d+)?:\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "code": 4,
+                    "message": 5
+                }
+            }
+        },
+        {
+            "label": "Configure cisTEM DEBUG build with LibTorch",
+            "type": "shell",
+            "command": "mkdir -p ${build_dir}/intel-gpu-debug-static-libtorch && cd ${build_dir}/intel-gpu-debug-static-libtorch && CC=icc CXX=icpc ../../configure ${input:additional_compiler_flags} --enable-debugmode --enable-gpu-debug --with-wx-config=/opt/WX/icc-static/bin/wx-config --enable-staticmode --with-cuda=${cuda_dir} --enable-libtorch ${experimental_algo_flags} ${common_optional_programs}  ${common_flags} "
+        },
+        {
+            "label": "BUILD cisTEM DEBUG with LibTorch",
+            "type": "shell",
+            "command": "cd ${build_dir}/intel-gpu-debug-static-libtorch && make -j${input:compile_cores} 2>&1 | sed -u 's|../../../src/|${workspaceFolder}/src/|g' && mkdir -p src/lib && cp -u /opt/libtorch/lib/libtorch.so* /opt/libtorch/lib/libtorch_cpu.so* /opt/libtorch/lib/libc10.so* /opt/libtorch/lib/libgomp*.so* src/lib/ 2>/dev/null || true",
+            "problemMatcher": {
+                "owner": "icpc",
+                "fileLocation": "absolute",
+                "pattern": {
+                    "regexp": "^(.*)\\((\\d+)\\):\\s+(warning|error|remark)\\s+#?(\\d+)?:\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "code": 4,
+                    "message": 5
+                }
+            }
         },
         {
             "label": "CONFIG GNU, gpu",