Merge pull request #3 from mbuze/release-v0.2.0

Release v0.2.0

Author: mbuze

.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      KEOPS_VERBOSE: "0"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: pip
+      - name: Install CPU-only PyTorch
+        run: pip install torch --index-url https://download.pytorch.org/whl/cpu
+      - name: Install remaining dependencies
+        run: |
+          grep -v '^torch' requirements.txt > /tmp/req-notorch.txt
+          pip install -r /tmp/req-notorch.txt && pip install -e .
+      - name: Lint
+        run: ruff check .
+      - name: Run tests
+        run: pytest

.gitignore

@@ -10,3 +10,10 @@ notebooks/extensions
 **/__pycache__/
 
 .tmp.*
+
+.vscode/
+
+.pytest_cache/
+.ruff_cache/
+
+notebooks/tutorials/outputs/

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.0
+    hooks:
+      - id: ruff          # lint (with --fix)
+        args: [--fix]
+      - id: ruff-format   # format

PyAPD/__init__.py

@@ -1,17 +1,48 @@
-from .geometry_utils import *
-#from .plotting_utils import *
-from .override_optimality_condition import *
-#from .pixel_method import *
-#from .esdot_method import *
-#from .sinkhorn import *
-from .ebsd_utils import *
-from .apds import *
-from .log_res import *
-from .log_res_utils import *
-
-
-# __all__ = ["geometry_utils",
-#            "plotting_utils",
-#            "pixel_method",
-#            "esdot_method"]
-
+from . import (
+    override_optimality_condition as override_optimality_condition,  # side-effect: patches torchmin
+)
+from .apds import apd_system as apd_system
+from .ebsd_utils import load_setup_from_EBSD_data_2D as load_setup_from_EBSD_data_2D
+from .geometry_utils import (
+    convert_axes_and_angle_to_matrix_2D as convert_axes_and_angle_to_matrix_2D,
+)
+from .geometry_utils import (
+    initial_guess_heuristic as initial_guess_heuristic,
+)
+from .geometry_utils import (
+    sample_normalised_spd_matrices as sample_normalised_spd_matrices,
+)
+from .geometry_utils import (
+    sample_seeds_with_exclusion as sample_seeds_with_exclusion,
+)
+from .geometry_utils import (
+    sample_spd_matrices_perturbed_from_identity as sample_spd_matrices_perturbed_from_identity,
+)
+from .geometry_utils import (
+    specify_volumes as specify_volumes,
+)
+from .log_res import min_diagram_system as min_diagram_system
+from .log_res_utils import (
+    assemble_design_matrix as assemble_design_matrix,
+)
+from .log_res_utils import (
+    calculate_moments_from_data as calculate_moments_from_data,
+)
+from .log_res_utils import (
+    convert_from_lr_to_phys as convert_from_lr_to_phys,
+)
+from .log_res_utils import (
+    convert_from_phys_to_lr as convert_from_phys_to_lr,
+)
+from .log_res_utils import (
+    convert_theta_between_bases as convert_theta_between_bases,
+)
+from .log_res_utils import (
+    gridify_Y_I as gridify_Y_I,
+)
+from .log_res_utils import (
+    physical_heuristic_guess as physical_heuristic_guess,
+)
+from .log_res_utils import (
+    reorder_variables as reorder_variables,
+)