Add CI configuration

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yml

@@ -0,0 +1,56 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - 'v[0-9]*'
+    tags:
+      - 'v[0-9]*'
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    strategy:
+      matrix:
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, windows-latest, macos-14]
+        exclude:
+          - os: macos-14
+            python_version: "3.9"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Choose Python version ${{ matrix.python_version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: '${{ matrix.python_version }}'
+      - name: install the package
+        run: python3 -m pip install .[test]
+      - name: run pytest
+        run: pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
+      - name: submit code coverage
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  numba_coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: 'Choose Python version 3.12'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: install the package
+        run: python3 -m pip install .[test]
+      - name: run pytest
+        run: NUMBA_DISABLE_JIT=1 pytest --cov=microscope_calibration --cov-report=xml --cov-report=term tests/
+      - name: submit code coverage
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.1
+  hooks:
+    - id: pyupgrade
+      args: ["--py39-plus"]

packaging/.gitignore

@@ -1,2 +1 @@
 Microscope-Calibration
-

packaging/build.sh

@@ -6,5 +6,5 @@ mkdir packaging/Microscope-Calibration; \
 git archive --format=tar HEAD | tar xvf - -C packaging/Microscope-Calibration \
 )
 
-apptainer build --force overfocus.sif overfocus.def 
+apptainer build --force overfocus.sif overfocus.def
 apptainer overlay create --size 1024 overfocus.sif

packaging/run.sh

@@ -1,3 +1,2 @@
 #!/bin/sh
 apptainer run --writable overfocus.sif
-

packaging/update-requirements.sh

@@ -1,3 +1,2 @@
 #!/bin/sh
 uv pip compile --python-version=3.11 requirements.in ../pyproject.toml > requirements.txt
-

pyproject.toml

@@ -7,24 +7,23 @@ name = "microscope-calibration"
 description = "Tools to calibrate a microscope"
 license = {file = "LICENSE"}
 keywords = ["microscopy", "LiberTEM", "TEM", "STEM"]
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 dynamic = ["version", "readme"]
 dependencies = [
     "numpy",
     "libertem",
     "typing-extensions",
-    "temgymbasic@git+https://github.com/TemGym/TemGym",
+    "temgymbasic@git+https://github.com/TemGym/TemGym@03062b098a50ea72f0ae9a2438b861d7a62691ee",
     "numba",
     "scikit-image",
     "scipy",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Development Status :: 3 - Alpha",
 ]
 authors = [
@@ -35,7 +34,7 @@ authors = [
 repository = "https://github.com/LiberTEM/Microscope-Calibration"
 
 [project.optional-dependencies]
-test = ["pytest"]
+test = ["pytest", "pytest-cov"]
 
 [tool.setuptools.dynamic]
 version = {attr = "microscope_calibration.__version__"}

src/microscope_calibration/util/optimize.py

@@ -1,7 +1,8 @@
 import numpy as np
 from scipy. optimize import shgo
 from skimage.measure import blur_effect
-from typing import TYPE_CHECKING, Iterable, Callable, Optional
+from typing import TYPE_CHECKING, Callable, Optional
+from collections.abc import Iterable
 
 from microscope_calibration.common.stem_overfocus import OverfocusParams
 

src/microscope_calibration/util/stem_overfocus_sim.py

@@ -21,7 +21,7 @@ def smiley(size):
     y, x = np.ogrid[-size//2:size//2, -size//2:size//2]
 
     outline = (((y*1.2)**2 + x**2) > (110/256*size)**2) & \
-              ((((y*1.2)**2 + x**2) < (120/256*size)**2))
+              (((y*1.2)**2 + x**2) < (120/256*size)**2)
     obj[outline] = 0.0
 
     left_eye = ((y + 40/256*size)**2 + (x + 40/256*size)**2) < (20/256*size)**2
@@ -35,7 +35,7 @@ def smiley(size):
     obj[nose] = (0.05j * x + 0.05j * y)[nose]
 
     mouth = (((y*1)**2 + x**2) > (50/256*size)**2) & \
-            ((((y*1)**2 + x**2) < (70/256*size)**2)) & \
+            (((y*1)**2 + x**2) < (70/256*size)**2) & \
             (y > 20/256*size)
 
     obj[mouth] = 0

tests/test_overfocus.py

@@ -9,7 +9,7 @@
 from microscope_calibration.common.stem_overfocus import (
     OverfocusParams, make_model, get_translation_matrix
 )
-from microscope_calibration.util.optimize import make_overfocus_loss_function, minimize
+from microscope_calibration.util.optimize import make_overfocus_loss_function, optimize
 
 from microscope_calibration.udf.stem_overfocus import OverfocusUDF
 from libertem.api import Context
@@ -441,14 +441,14 @@ def test_optimize():
         dataset=ds,
         overfocus_udf=ref_udf,
     )
-    res = minimize(loss=loss)
+    res = optimize(loss=loss)
     res_params = make_new_params(res.x)
     assert_allclose(res_params['scan_rotation'], params['scan_rotation'], atol=0.1)
     assert_allclose(res_params['overfocus'], params['overfocus'], rtol=0.1)
 
     valdict = {'val': False}
 
-    def callback(args, new_params, udf_results):
+    def callback(args, new_params, udf_results, current_loss):
         if valdict['val']:
             pass
         else:
@@ -467,7 +467,10 @@ def callback(args, new_params, udf_results):
         extra_udfs=(OverfocusUDF(params), ),
         plots=(),
     )
-    res = minimize(loss=loss, method='SLSQP', bounds=[(-10, 10), (-10, 10)])
+    res = optimize(
+        loss=loss, minimizer_kwargs={'method': 'SLSQP'},
+        bounds=[(-10, 10), (-10, 10)],
+    )
     res_params = make_new_params(res.x)
     assert_allclose(res_params['scan_rotation'], params['scan_rotation'], atol=0.1)
     assert_allclose(res_params['overfocus'], params['overfocus'], rtol=0.1)