In depth upgrades

.github/workflows/ci-cd.yml

@@ -26,6 +26,10 @@ jobs:
     uses: ./.github/workflows/build.yml
     secrets: inherit
 
+  standalone:
+    needs: [tests]
+    uses: ./.github/workflows/standalone.yml
+
   docs:
     needs: [release]  # get (release) version number first
     uses: ./.github/workflows/docs.yml

.github/workflows/standalone.yml

@@ -0,0 +1,136 @@
+name: Standalone
+
+on:
+  workflow_call:
+    inputs:
+      mcsas3_ref:
+        description: McSAS3 ref to check out. Defaults to the current GUI branch, then main.
+        required: false
+        type: string
+  workflow_dispatch:
+    inputs:
+      mcsas3_ref:
+        description: McSAS3 ref to check out. Defaults to the current GUI branch, then main.
+        required: false
+        type: string
+
+jobs:
+  standalone:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: Checking out the GUI repo
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Check out McSAS3
+        uses: actions/checkout@v5
+        with:
+          repository: ${{ github.repository_owner }}/McSAS3
+          path: McSAS3
+          ref: ${{ inputs.mcsas3_ref || github.head_ref || github.ref_name || 'main' }}
+
+      - name: Show selected dependency refs
+        shell: bash
+        run: |
+          set -euxo pipefail
+          echo "McSAS3 ref: ${{ inputs.mcsas3_ref || github.head_ref || github.ref_name || 'main' }}"
+
+      - name: Setting up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: |
+            ci/requirements.txt
+            pyproject.toml
+            tox.ini
+
+      - name: Install required system packages
+        shell: bash
+        run: |
+          set -euxo pipefail
+          PLATFORM="$(echo "$RUNNER_OS" | tr '[:upper:]' '[:lower:]')"
+          REQFN="ci/requirements_${PLATFORM}.txt"
+          if [[ "$PLATFORM" == "linux" && -f "$REQFN" ]]; then
+            mapfile -t packages < <(grep -vE '^\s*(#|$)' "$REQFN")
+            if [[ "${#packages[@]}" -gt 0 ]]; then
+              sudo apt-get update
+              sudo apt-get -y install "${packages[@]}"
+            fi
+          else
+            echo "No extra standalone system packages declared for $PLATFORM."
+          fi
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          set -euxo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install --progress-bar=off -r ci/requirements.txt
+
+      - name: Build standalone GUI bundle
+        shell: bash
+        env:
+          MCSAS3GUI_MCSAS3_SRC: ${{ github.workspace }}/McSAS3/src
+        run: tox -e standalone -v
+
+      - name: Verify standalone bundle manifest
+        shell: bash
+        run: |
+          set -euxo pipefail
+          python - <<'PY'
+          import json
+          import platform
+          from pathlib import Path
+
+          system = platform.system().lower()
+          machine = platform.machine().lower().replace("x86_64", "amd64")
+          platform_tag = f"{system}-{machine}"
+          bundle_root = Path("dist") / "standalone" / platform_tag
+          build_info = bundle_root / "build_info.json"
+          readme = bundle_root / "README_STANDALONE.txt"
+          archive = Path("dist") / "standalone" / f"mcsas3gui-standalone-{platform_tag}.zip"
+
+          if not bundle_root.is_dir():
+              raise SystemExit(f"Missing standalone bundle root: {bundle_root}")
+          if not readme.is_file():
+              raise SystemExit(f"Missing bundle README: {readme}")
+          if not build_info.is_file():
+              raise SystemExit(f"Missing build manifest: {build_info}")
+          if not archive.is_file():
+              raise SystemExit(f"Missing standalone archive: {archive}")
+
+          payload = json.loads(build_info.read_text(encoding="utf-8"))
+          expected_platform = platform_tag
+          if payload["platform"] != expected_platform:
+              raise SystemExit(
+                  f"Build manifest platform mismatch: {payload['platform']} != {expected_platform}"
+              )
+
+          gui_bundle = bundle_root / payload["gui_bundle"]
+          gui_executable = bundle_root / payload["gui_executable"]
+          histogrammer = bundle_root / payload["bundled_histogrammer"]
+
+          if not gui_bundle.exists():
+              raise SystemExit(f"Missing GUI bundle: {gui_bundle}")
+          if not gui_executable.is_file():
+              raise SystemExit(f"Missing GUI executable: {gui_executable}")
+          if not histogrammer.is_file():
+              raise SystemExit(f"Missing bundled histogram helper: {histogrammer}")
+          PY
+
+      - name: Upload standalone artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: standalone-${{ matrix.os }}
+          path: |
+            dist/standalone/*.zip
+            dist/standalone/*/README_STANDALONE.txt
+            dist/standalone/*/build_info.json

.github/workflows/tests.yml

@@ -2,10 +2,19 @@ name: Tests
 
 # Controls when the action will run.
 on:
+  workflow_call:
+    inputs:
+      mcsas3_ref:
+        description: McSAS3 ref to check out. Defaults to the current GUI branch, then main.
+        required: false
+        type: string
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-
-  workflow_call:
+    inputs:
+      mcsas3_ref:
+        description: McSAS3 ref to check out. Defaults to the current GUI branch, then main.
+        required: false
+        type: string
 
 jobs:
   # defining this job separately allows to refer to it later as job.needs dependency
@@ -20,8 +29,9 @@ jobs:
         # os: ['ubuntu', 'windows', 'macos']
         os: ['windows']
     env:
-      PYTHON: ${{ join(matrix.python, '.') }}  # e.g. '3.11'
-      TOX_ENV: ${{ format('{0}{1}', 'py', join(matrix.python, '')) }}  # e.g. 'py311'
+      PYTHON: ${{ join(matrix.python, '.') }}  # e.g. '3.12'
+      TOX_ENV: ${{ format('{0}{1}', 'py', join(matrix.python, '')) }}  # e.g. 'py312'
+      MCSAS3GUI_MCSAS3_SRC: ${{ github.workspace }}/McSAS3/src
     runs-on: ${{ format('{0}-latest', matrix.os) }}
     name: "Test py-${{ join(matrix.python, '.') }} (${{ matrix.os }})"
     steps:
@@ -30,7 +40,13 @@ jobs:
         uses: actions/checkout@v5
         with:
           fetch-depth: 0
-          ref: main
+
+      - name: Check out McSAS3
+        uses: actions/checkout@v5
+        with:
+          repository: ${{ github.repository_owner }}/McSAS3
+          path: McSAS3
+          ref: ${{ inputs.mcsas3_ref || github.head_ref || github.ref_name || 'main' }}
 
       - name: Setting up Python ${{ env.PYTHON }}
         uses: actions/setup-python@v5

.gitignore

@@ -1,5 +1,6 @@
 *.py[cod]
 __pycache__
+uv.lock
 
 # C extensions
 *.so
@@ -107,9 +108,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
 #  you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 
@@ -136,3 +137,34 @@ temporary_files/run.yaml
 temporary_files/data.yaml
 logs/mcsas3_debug.log
 logs/mcsas3_debug.log
+read_configurations/Moeez_csv.yaml
+read_configurations/Moeez_S171.yaml
+run_configurations/run_config_Moeez_longcyl.yaml
+run_configurations/run_config_Moeez.yaml
+src/mcsas3gui/configurations/histogram/hist_config_dual_KJ.yaml
+src/mcsas3gui/configurations/histogram/hist_config_dual_kuanode.yaml
+src/mcsas3gui/configurations/histogram/hist_dual_tomek.yaml
+src/mcsas3gui/configurations/readdata/read_kuehns_nxs_data.yaml
+src/mcsas3gui/configurations/readdata/read_Pauls_base_mats_dat.yaml
+src/mcsas3gui/configurations/readdata/read_Pauls_kuanode_kapton_dat.yaml
+src/mcsas3gui/configurations/readdata/read_Pauls_kuanode_kapton_nxs.yaml
+src/mcsas3gui/configurations/readdata/read_tomeks_csv.yaml
+src/mcsas3gui/configurations/run/run_config_kuanode.yaml
+src/mcsas3gui/configurations/run/run_config_kuehn.yaml
+src/mcsas3gui/configurations/run/run_config_pauls_base_moar.yaml
+src/mcsas3gui/configurations/run/run_config_pauls_base.yaml
+src/mcsas3gui/configurations/run/run_config_tomek.yaml
+testdata/Archive.zip
+testdata/Example_cyl_output.hdf5
+testdata/Example_cyl_output.pdf
+testdata/Example_output.hdf5
+testdata/Example_output.pdf
+testdata/Example.csv
+testdata/merged_AutoMOFs_7_L011_output.hdf5
+testdata/merged_AutoMOFs_7_L011_output.pdf
+testdata/quickstartdemo1_output.hdf5
+testdata/quickstartdemo1_output.pdf
+testdata/round_robin_dataset_1_output.hdf5
+testdata/round_robin_dataset_1_output.pdf
+testdata/round_robin_dataset_3_output.hdf5
+testdata/round_robin_dataset_3_output.pdf

.pre-commit-config.yaml

@@ -10,15 +10,9 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.8
     hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-      - id: black
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright © 2024 
+Copyright © 2024
 
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -19,4 +19,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+THE SOFTWARE.

MANIFEST.in

@@ -8,14 +8,36 @@ include .editorconfig
 include .pre-commit-config.yaml
 include .copier-answers.yml
 include tox.ini
+include *.spec
 include templates/*.j2
+recursive-include tools *.py
 include notebooks/*.ipynb
+recursive-include read_configurations *.yaml
+recursive-include run_configurations *.yaml
 
 include README.md
 include CHANGELOG.md
 include AUTHORS.rst
 include CONTRIBUTING.rst
 include LICENSE
 
+exclude src/mcsas3gui/configurations/histogram/hist_config_dual_KJ.yaml
+exclude src/mcsas3gui/configurations/histogram/hist_config_dual_kuanode.yaml
+exclude src/mcsas3gui/configurations/histogram/hist_dual_tomek.yaml
+exclude src/mcsas3gui/configurations/readdata/read_kuehns_nxs_data.yaml
+exclude src/mcsas3gui/configurations/readdata/read_Pauls_base_mats_dat.yaml
+exclude src/mcsas3gui/configurations/readdata/read_Pauls_kuanode_kapton_dat.yaml
+exclude src/mcsas3gui/configurations/readdata/read_Pauls_kuanode_kapton_nxs.yaml
+exclude src/mcsas3gui/configurations/readdata/read_tomeks_csv.yaml
+exclude src/mcsas3gui/configurations/run/run_config_kuanode.yaml
+exclude src/mcsas3gui/configurations/run/run_config_kuehn.yaml
+exclude src/mcsas3gui/configurations/run/run_config_pauls_base.yaml
+exclude src/mcsas3gui/configurations/run/run_config_pauls_base_moar.yaml
+exclude src/mcsas3gui/configurations/run/run_config_tomek.yaml
+exclude read_configurations/Moeez_S171.yaml
+exclude read_configurations/Moeez_csv.yaml
+exclude run_configurations/run_config_Moeez.yaml
+exclude run_configurations/run_config_Moeez_longcyl.yaml
+
 global-exclude *.py[cod] __pycache__/* *.so *.dylib .DS_Store */.ipynb_checkpoints/* .*.kate-swp
 global-exclude *.afdesign

McSAS3GUI.spec

@@ -0,0 +1,50 @@
+# -*- mode: python ; coding: utf-8 -*-
+
+
+a = Analysis(
+    ['src/mcsas3gui/main.py'],
+    pathex=[],
+    binaries=[],
+    datas=[],
+    hiddenimports=[],
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    noarchive=False,
+    optimize=0,
+)
+pyz = PYZ(a.pure)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='McSAS3GUI',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=False,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='McSAS3GUI',
+)
+app = BUNDLE(
+    coll,
+    name='McSAS3GUI.app',
+    icon=None,
+    bundle_identifier=None,
+)