Ctf3d ci

.devcontainer/.MakeParticleStack.dff

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+Read coordinates from file?:: yes
+X-dimension of original MIP:: 5760
+Y-dimension of original MIP:: 4092
+Input x,y,z coordinate file:: /home/himesb/tmp/coords_prepare_no_upsample.txt
+Input image file:: image.mrc
+Output star file:: /home/himesb/tmp/from_coords.star
+Output particle stack:: /home/himesb/tmp/from_coords.mrc
+Box size for particles (px.):: 256
+Pixel size of image (A):: 1.0
+Average defocus 1 (A):: 5000.0
+Average defocus 2 (A):: 5000.0
+Average defocus angle (deg):: 0.0
+Beam energy (keV):: 300.0
+Spherical aberration (mm):: 2.7
+Amplitude contrast:: 0.07

.devcontainer/check-version.sh

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+#!/usr/bin/env bash
+# Check if devcontainer image version matches CONTAINER_VERSION_TOP
+# Fails by default - only passes on explicit version match
+
+# EARLY MARKER: Write immediately to prove script was invoked
+{
+    echo "=========================================="
+    echo "INVOKED: $(date '+%Y-%m-%d %H:%M:%S')"
+    echo "PWD: $(pwd)"
+    echo "Script path: $0"
+    echo "BASH_SOURCE: ${BASH_SOURCE[0]}"
+    echo "=========================================="
+} >> /tmp/devcontainer-check-invoked.log
+
+set -e  # Exit on any error
+
+# Setup logging - write to file directly at each echo
+LOG_FILE="/tmp/devcontainer-version-check-$(date +%s).log"
+
+# Helper function to log to both stdout and file
+log() {
+    #echo "$@"
+    echo "$@" >> "${LOG_FILE}"
+}
+
+# Initialize log file
+echo "Script started: $(date '+%Y-%m-%d %H:%M:%S')" > "${LOG_FILE}"
+
+# Get the directory where this script is located
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+WORKSPACE_ROOT="$(dirname "$SCRIPT_DIR")"
+
+log "=================================================="
+log "DevContainer Version Check"
+log "=================================================="
+log "Timestamp: $(date '+%Y-%m-%d %H:%M:%S')"
+log "Log file: ${LOG_FILE}"
+log ""
+log "📂 Workspace root: ${WORKSPACE_ROOT}"
+
+VERSION_FILE="${WORKSPACE_ROOT}/.vscode/CONTAINER_VERSION_TOP"
+REPO_FILE="${WORKSPACE_ROOT}/.vscode/CONTAINER_REPO_NAME"
+DEVCONTAINER_FILE="${WORKSPACE_ROOT}/.devcontainer/devcontainer.json"
+
+log "📄 Checking version file: ${VERSION_FILE}"
+log "📄 Checking repo file: ${REPO_FILE}"
+log "📄 Checking devcontainer file: ${DEVCONTAINER_FILE}"
+
+# Verify required files exist
+if [ ! -f "$VERSION_FILE" ]; then
+    log ""
+    log "❌ ERROR: CONTAINER_VERSION_TOP file not found at: $VERSION_FILE"
+    log "   This file is required to validate container version."
+    exit 1
+fi
+
+if [ ! -f "$REPO_FILE" ]; then
+    log ""
+    log "❌ ERROR: CONTAINER_REPO_NAME file not found at: $REPO_FILE"
+    log "   This file is required to validate container repository."
+    exit 1
+fi
+
+if [ ! -f "$DEVCONTAINER_FILE" ]; then
+    log ""
+    log "❌ ERROR: devcontainer.json not found at: $DEVCONTAINER_FILE"
+    exit 1
+fi
+
+# Read expected values from config files
+EXPECTED_VERSION=$(cat "$VERSION_FILE" | tr -d '[:space:]')
+EXPECTED_REPO=$(cat "$REPO_FILE" | tr -d '[:space:]')
+
+if [ -z "$EXPECTED_VERSION" ]; then
+    log ""
+    log "❌ ERROR: CONTAINER_VERSION_TOP file is empty"
+    log "   The version file must contain a valid version number."
+    exit 1
+fi
+
+if [ -z "$EXPECTED_REPO" ]; then
+    log ""
+    log "❌ ERROR: CONTAINER_REPO_NAME file is empty"
+    log "   The repo file must contain a valid repository path."
+    exit 1
+fi
+
+# Construct expected image string
+EXPECTED_IMAGE="${EXPECTED_REPO}:v${EXPECTED_VERSION}"
+
+# Extract current image from devcontainer.json
+CURRENT_IMAGE=$(grep -oP '"image":\s*"\K[^"]+' "$DEVCONTAINER_FILE")
+
+log ""
+log "📋 CONTAINER_REPO_NAME specifies: ${EXPECTED_REPO}"
+log "📋 CONTAINER_VERSION_TOP specifies: v${EXPECTED_VERSION}"
+log "📋 Expected image: ${EXPECTED_IMAGE}"
+log ""
+log "🔧 devcontainer.json image field: ${CURRENT_IMAGE}"
+
+log ""
+log "🔍 Comparing images..."
+log "   Expected: ${EXPECTED_IMAGE}"
+log "   Current:  ${CURRENT_IMAGE}"
+
+# Compare images
+if [ "$EXPECTED_IMAGE" != "$CURRENT_IMAGE" ]; then
+    log ""
+    log "❌ ERROR: Image mismatch detected"
+    log "   devcontainer.json uses: ${CURRENT_IMAGE}"
+    log "   Expected image: ${EXPECTED_IMAGE}"
+    log ""
+    log "   Action required:"
+    log "   Update devcontainer.json image field to: ${EXPECTED_IMAGE}"
+    exit 1
+fi
+
+# Success case - images match
+log ""
+log "✅ Container image check passed: ${EXPECTED_IMAGE}"
+log "=================================================="
+exit 0

.devcontainer/configure-git.sh

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+#!/usr/bin/env bash
+#
+# Configure git identity inside the devcontainer.
+#
+# Priority:
+#   1. GIT_AUTHOR_NAME / GIT_AUTHOR_EMAIL env vars (if set)
+#   2. Fall through — let VS Code's default forwarding handle it
+#
+# Called by devcontainer.json postCreateCommand.
+
+configure_if_unset() {
+    local current_name current_email
+
+    current_name="$(git config --global user.name 2>/dev/null)"
+    current_email="$(git config --global user.email 2>/dev/null)"
+
+    # If git identity is already configured (e.g., VS Code forwarded it), done
+    if [ -n "$current_name" ] && [ -n "$current_email" ]; then
+        echo "Git identity already configured: ${current_name} <${current_email}>"
+        return 0
+    fi
+
+    # Try env vars
+    if [ -n "$GIT_AUTHOR_NAME" ] && [ -n "$GIT_AUTHOR_EMAIL" ]; then
+        git config --global user.name "$GIT_AUTHOR_NAME"
+        git config --global user.email "$GIT_AUTHOR_EMAIL"
+        echo "Git identity set from env: ${GIT_AUTHOR_NAME} <${GIT_AUTHOR_EMAIL}>"
+        return 0
+    fi
+
+    echo "WARNING: Git identity not configured."
+    echo "  Set GIT_AUTHOR_NAME and GIT_AUTHOR_EMAIL in devcontainer.json remoteEnv,"
+    echo "  or configure git globally on your local machine."
+    return 0  # Non-fatal — don't block container creation
+}
+
+configure_if_unset

.devcontainer/devcontainer.json

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+{
+  "name": "cisTEMx-${localEnv:USER}-${localWorkspaceFolderBasename}",
+  "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind,consistency=cached",
+  "workspaceFolder": "${localWorkspaceFolder}",
+  // NOTE: Container image must match .vscode/CONTAINER_REPO_NAME and CONTAINER_VERSION_TOP
+  // Update all three when changing container version or repository
+  "image": "ghcr.io/stochasticanalytics/cistem_build_env:v4.0.0",
+  "initializeCommand": ".devcontainer/check-version.sh",
+  "postCreateCommand": "bash .devcontainer/configure-git.sh && source ~/.nvm/nvm.sh && npm install -g @anthropic-ai/sandbox-runtime pyright typescript-language-server typescript",
+  "remoteUser": "cisTEMdev",
+  "hostRequirements": {
+    "gpu": "optional"
+  },
+  "remoteEnv": {
+    // We need to set this so we can use wxmctrl -lpx | grep ${WORKSPACE_BASENAME} | awk '{print $1}' to find window IDs
+    // then xdotool get_desktop_for_window <windowID> to get the desktop number
+    // then later compare to xdotool get_desktop to see if the window is on the current desktop, if not we can run a hook to push notify if claude is read.
+    // FIXME this should just come from name
+    "WORKSPACE_BASENAME": "${localWorkspaceFolderBasename}",
+    "WORKSPACE_CONTAINER_NAME": "cisTEMx-${localEnv:USER}-${localWorkspaceFolderBasename}",
+    // Persist Claude Code sessions, plans, and memories across container rebuilds
+    "CLAUDE_CONFIG_DIR": "/sa_shared/.claude"
+  },
+  // To add mounts, enable smudge/clean filters, define variable in bashrc ... cistem_mounts=("source=/scratch,target=/scratch,type=bind" "source=/sa_shared,target=/sa_shared,type=bind")"
+  // Leave the following line comment, it is used as a placeholder for the devcontainer-filter.sh script to insert the mounts.
+  // begin_mounts
+  "mounts": [
+    "source=/scratch,target=/scratch,type=bind",
+    "source=/sa_shared,target=/sa_shared,type=bind"
+  ],
+  // end_mounts
+  // UID is 1000 in base container (default)
+  "updateRemoteUserUID": false,
+  // Network configuration: Using host networking for maximum compatibility.
+  // Whisper Assistant server runs on separate whisper-net bridge network with port 4444 exposed to host.
+  // This devcontainer accesses whisper via localhost:4444 through host network.
+  "runArgs": [
+    "--gpus",
+    "all",
+    "--security-opt",
+    "apparmor=unconfined",
+    "-it",
+    "--net",
+    "host",
+    "-e",
+    "DISPLAY=${env:DISPLAY}",
+    "-v",
+    "${env:XAUTHORITY}:/home/cisTEMdev/.Xauthority",
+    "-v",
+    "/tmp/.X11-unix:/tmp/.X11-unix"
+  ],
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "maelvalais.autoconf",
+        "ms-python.autopep8",
+        "ms-vscode.cpptools",
+        "ms-vscode.cpptools-extension-pack",
+        "cschlosser.doxdocgen",
+        "eamodio.gitlens",
+        "DavidAnson.vscode-markdownlint",
+        "ms-python.vscode-pylance",
+        "ms-python.python",
+        "frinkr.vscode-tabify",
+        "jomeinaster.bracket-peek",
+        "onnovalkering.vscode-singularity"
+      ]
+    }
+  }