python-microscopy · David-Baddeley · Aug 21, 2026 · Aug 21, 2026 · Aug 21, 2026
diff --git a/.github/workflows/build_pip.yml b/.github/workflows/build_pip.yml
@@ -4,14 +4,17 @@
 name: Build PIP packages
 
 on:
-  release:
-    types: [created, edited]
-
+  workflow_run:
+    workflows: ["Make release"]
+    types: [completed]
   workflow_dispatch:
 
 jobs:
   deploy_source:
     runs-on: 'macos-latest'
+    if: >
+      github.event_name == 'workflow_dispatch' ||
+      github.event.workflow_run.conclusion == 'success'
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.github/workflows/make_installers.yaml b/.github/workflows/make_installers.yaml
@@ -0,0 +1,56 @@
+name: Build Installers
+
+on:
+  workflow_run:
+    workflows: ["Build PIP packages"]
+    types: [completed]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  windows:
+    runs-on: windows-latest
+    if: >
+      github.event_name == 'workflow_dispatch' ||
+      github.event.workflow_run.conclusion == 'success'
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build bundle
+        shell: cmd
+        run: installers\install-python-microscopy.bat bundle
+
+      - name: Get installed version
+        id: version
+        shell: pwsh
+        run: |
+          $v = & "bundle\venv\Scripts\python.exe" `
+            -c "import importlib.metadata; print(importlib.metadata.version('python-microscopy'))"
+          "version=$v" | Out-File -FilePath $env:GITHUB_OUTPUT -Append
+
+      - name: Build installer
+        shell: pwsh
+        run: |
+          & "C:\Program Files (x86)\Inno Setup 6\ISCC.exe" `
+            /DAppSourceDir="$env:GITHUB_WORKSPACE\bundle" `
+            /DAppVersion="${{ steps.version.outputs.version }}" `
+            installers\windows\pyme_setup.iss
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: PYME-${{ steps.version.outputs.version }}-windows-installer
+          path: installers\windows\Output\PYME-*-setup.exe
+
+      - name: Attach to release
+        if: github.event_name == 'workflow_run'
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ steps.version.outputs.version }}
+          files: installers/windows/Output/PYME-*-setup.exe
diff --git a/installers/INSTALLERS.md b/installers/INSTALLERS.md
@@ -0,0 +1,24 @@
+# Single-click / non expert installers
+This folder contains the code to create installers for windows and mac.
+
+
+## Commonalities
+- A script (or potentiall similar bash/powershell/bat scritps) to construct a self contained folder with python and PYME.
+- the script should use uv to create an enviroment and install the current pip PYME package in it, relying on that package to determine any additional dependencies
+- the script should accept a parameter for the output folder, defaulting to creating a `PYME` directory in the users home directory.
+- download (curl) uv if not already installed.
+- The script should idealy create executable top level aliases to PYMEAcquire, PYMEImage, PYMEVis and PYMEClusterOfOne (as defined in the pyproject.toml scripts section). The script should also create a alias activating venv for console use.
+- Python version is defined by an easily editable TARGET_PYTHON, with an initial target of 3.13 - potentially in installer_defines.yaml or a an alternative readily (minimal external deps) cross-platform format. We ahould also put the list of entry points to expose in here (which are expected to be a subset of the entrypoints defined in pyproject.toml).
+- this script acts as the default installer while we build the more native windows and mac options, and remains the installation script for linux.
+
+
+## Windows
+- Use InnoSetup to create an executable installer, from the bundle created by the common script
+- Start menu group PYME, with shortcuts to the top level entry points as described above, and a `PYME Console` shortcut to create a shell with the venv active.
+- File associations to be revisited after basics working.
+- Ideally install for me only and all users options.
+- This will eventually run in a github action on windows-latest (which should already have inno setup available).
+
+## Mac
+- Ultimate goal is an app package, derived from bundle, with appropriate entry points.
+- Parked for now pending to a bit more research, but avoid things in script structure which will bite us on that later.
diff --git a/installers/install-python-microscopy.bat b/installers/install-python-microscopy.bat
@@ -0,0 +1,82 @@
+@echo off
+setlocal EnableDelayedExpansion
+
+:: ---- Config (mirrors installer_defines.sh — keep in sync) ----
+set "TARGET_PYTHON=3.13"
+set "PACKAGE_NAME=python-microscopy"
+set "ENTRY_POINTS=PYMEAcquire PYMEImage PYMEVis PYMEClusterOfOne"
+set "DEFAULT_DEST=%USERPROFILE%\PYME"
+
+:: ---- Destination (first positional arg, else default) ----
+if not "%~1"=="" (set "DEST=%~1") else (set "DEST=%DEFAULT_DEST%")
+echo Installing PYME to: !DEST!
+if not exist "!DEST!\" mkdir "!DEST!"
+
+:: ---- Locate or download uv ----
+:: Context A (CI): uv is in PATH via astral-sh/setup-uv action — the where check passes immediately.
+:: Context B (end-user): uv.exe is downloaded to DEST\bin\ and used from there.
+where uv >nul 2>&1
+if not errorlevel 1 (
+    set "UV=uv"
+) else (
+    call :download_uv
+    if errorlevel 1 exit /b 1
+)
+
+:: ---- Managed Python + virtual environment ----
+echo Installing Python !TARGET_PYTHON!...
+"!UV!" python install !TARGET_PYTHON!
+if errorlevel 1 (echo ERROR: uv python install failed & exit /b 1)
+
+echo Creating virtual environment...
+"!UV!" venv --python !TARGET_PYTHON! "!DEST!\venv"
+if errorlevel 1 (echo ERROR: venv creation failed & exit /b 1)
+
+:: ---- Install PYME from pip ----
+echo Installing !PACKAGE_NAME!...
+"!UV!" pip install --python "!DEST!\venv\Scripts\python.exe" !PACKAGE_NAME!
+if errorlevel 1 (echo ERROR: package installation failed & exit /b 1)
+
+:: ---- Entry point .cmd wrappers ----
+for %%e in (%ENTRY_POINTS%) do call :mk_wrapper "%%e"
+
+:: ---- Activated-console helper ----
+(
+    echo @echo off
+    echo start cmd.exe /k "%%~dp0venv\Scripts\activate.bat"
+) > "!DEST!\pyme-console.cmd"
+
+echo.
+echo Installation complete.
+echo   Wrappers: %ENTRY_POINTS%
+echo   Add !DEST! to your PATH, or run the .cmd files directly.
+echo   Activated console: !DEST!\pyme-console.cmd
+goto :eof
+
+
+:: ----------------------------------------------------------------
+:download_uv
+:: Downloads uv.exe (x86-64) into DEST\bin\ via curl + PowerShell.
+:: Requires Windows 10 1803+ (curl.exe and tar.exe built-in).
+if not exist "!DEST!\bin\" mkdir "!DEST!\bin"
+set "UV_ZIP=%TEMP%\uv_download.zip"
+echo Downloading uv (x86-64)...
+curl -fsSLo "%UV_ZIP%" "https://github.com/astral-sh/uv/releases/latest/download/uv-x86_64-pc-windows-msvc.zip"
+if errorlevel 1 (echo ERROR: Failed to download uv & exit /b 1)
+powershell -NoProfile -Command "Expand-Archive -LiteralPath '%UV_ZIP%' -DestinationPath '!DEST!\bin' -Force"
+if errorlevel 1 (echo ERROR: Failed to extract uv & exit /b 1)
+del "%UV_ZIP%"
+set "UV=!DEST!\bin\uv.exe"
+exit /b 0
+
+
+:: ----------------------------------------------------------------
+:mk_wrapper
+:: Writes a thin .cmd shim that forwards all arguments to the venv entry point exe.
+:: Uses %~dp0 so wrappers work even if the install folder is moved.
+set "_EP=%~1"
+(
+    echo @echo off
+    echo "%%~dp0venv\Scripts\!_EP!.exe" %%*
+) > "!DEST!\!_EP!.cmd"
+exit /b 0
diff --git a/installers/install-python-microscopy.sh b/installers/install-python-microscopy.sh
@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+# Linux/Mac installer for PYME. Also serves as the Mac installer pending a native .app.
+# Usage: install-python-microscopy.sh [--dest <path>]   (default: ~/PYME)
+#
+# Context A (CI/dev): uv is expected to be in PATH already.
+# Context B (end-user): uv is bootstrapped via astral.sh if not found.
+set -euo pipefail
+
+# --- Configuration ---
+TARGET_PYTHON=3.13
+PACKAGE_NAME=python-microscopy
+ENTRY_POINTS=(PYMEAcquire PYMEImage PYMEVis PYMEClusterOfOne)
+DEFAULT_DEST="$HOME/PYME"
+
+DEST="$DEFAULT_DEST"
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --dest)   DEST="$2"; shift 2 ;;
+        --dest=*) DEST="${1#--dest=}"; shift ;;
+        -h|--help)
+            echo "Usage: $0 [--dest <path>]"
+            echo "  Installs PYME into a self-contained directory using uv."
+            echo "  Default: $DEFAULT_DEST"
+            exit 0 ;;
+        *) echo "Unknown argument: $1 (run '$0 --help' for usage)" >&2; exit 1 ;;
+    esac
+done
+
+DEST="${DEST/#\~/$HOME}"
+echo "==> Installing PYME to: $DEST"
+mkdir -p "$DEST"
+
+# --- Ensure uv is available ---
+if ! command -v uv &>/dev/null; then
+    echo "==> uv not found; downloading via astral.sh..."
+    curl -LsSf https://astral.sh/uv/install.sh | sh
+    # Add the two common install locations; one will contain the binary.
+    export PATH="$HOME/.local/bin:${CARGO_HOME:-$HOME/.cargo}/bin:$PATH"
+    if ! command -v uv &>/dev/null; then
+        echo "ERROR: uv installation failed or installed to an unexpected location." >&2
+        exit 1
+    fi
+fi
+
+# --- Managed Python ---
+uv python install "$TARGET_PYTHON"
+
+# --- Virtual environment ---
+uv venv --python "$TARGET_PYTHON" "$DEST/venv"
+
+# --- Install PYME from pip ---
+echo "==> Installing $PACKAGE_NAME..."
+uv pip install --python "$DEST/venv/bin/python" "$PACKAGE_NAME"
+
+# --- Top-level entry point symlinks ---
+for ep in "${ENTRY_POINTS[@]}"; do
+    ln -sf "$DEST/venv/bin/$ep" "$DEST/$ep"
+done
+
+# --- Activated-shell helper ---
+cat > "$DEST/pyme-shell" <<'SHELL_SCRIPT'
+#!/usr/bin/env bash
+PYME_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$PYME_DIR/venv/bin/activate"
+exec "${SHELL:-bash}"
+SHELL_SCRIPT
+chmod +x "$DEST/pyme-shell"
+
+echo ""
+echo "==> Done."
+echo "    Entry points: ${ENTRY_POINTS[*]}"
+echo "    Add to PATH:       export PATH=\"$DEST:\$PATH\""
+echo "    Activated shell:   $DEST/pyme-shell"
diff --git a/installers/windows/pyme_setup.iss b/installers/windows/pyme_setup.iss
@@ -0,0 +1,47 @@
+; PYME Windows Installer — produced by InnoSetup on windows-latest.
+;
+; Typical CI invocation (after running install.bat to create the bundle):
+;   set VERSION=<output of: python -c "import importlib.metadata; print(importlib.metadata.version('python-microscopy'))">
+;   ISCC.exe /DAppSourceDir=C:\path\to\bundle /DAppVersion=%VERSION% pyme_setup.iss
+
+#ifndef AppSourceDir
+  #define AppSourceDir "..\..\PYME_bundle"
+#endif
+#ifndef AppVersion
+  #define AppVersion "0.0.0"
+#endif
+
+#define AppName      "PYME"
+#define AppPublisher "Baddeley Lab, University of Auckland"
+; Icons ship with the package inside the venv tree.
+; pymeLogo.png has no .ico equivalent — pmanal.ico is used in its place.
+#define IconsDir     "{app}\venv\Lib\site-packages\PYME\resources\icons"
+
+[Setup]
+; AppId uniquely identifies this application for upgrades and uninstall — do not change.
+AppId={{8F3A2E1D-6B4C-4D9F-A7E2-3C1B5F8A2D6E}
+AppName={#AppName}
+AppVersion={#AppVersion}
+AppPublisher={#AppPublisher}
+DefaultDirName={autopf}\{#AppName}
+DefaultGroupName={#AppName}
+; Per-user install by default; elevation dialog allows all-users install.
+PrivilegesRequired=lowest
+PrivilegesRequiredOverridesAllowed=dialog
+OutputBaseFilename=PYME-{#AppVersion}-setup
+Compression=lzma2
+SolidCompression=yes
+WizardStyle=modern
+; Avoid prompting to close running apps — PYME processes are independent.
+CloseApplications=no
+
+[Files]
+Source: "{#AppSourceDir}\*"; DestDir: "{app}"; Flags: recursesubdirs createallsubdirs
+
+[Icons]
+Name: "{group}\PYMEAcquire";      Filename: "{app}\PYMEAcquire.cmd";      IconFilename: "{#IconsDir}\pmacquire.ico"
+Name: "{group}\PYMEImage";        Filename: "{app}\PYMEImage.cmd";        IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\PYMEVis";          Filename: "{app}\PYMEVis.cmd";          IconFilename: "{#IconsDir}\pmvis.ico"
+Name: "{group}\PYMEClusterOfOne"; Filename: "{app}\PYMEClusterOfOne.cmd"; IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\PYME Console";     Filename: "{app}\pyme-console.cmd";     IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\Uninstall PYME";   Filename: "{uninstallexe}"