Add basic CI workflow

.github/workflows/CI.yaml

@@ -0,0 +1,36 @@
+name: ci
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        py-version:
+          - '3.11' # Oldest supported
+          - '3.14' # Latest stable
+    name: Python ${{ matrix.py-version }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Use Python ${{ matrix.py-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.py-version }}
+          architecture: x64
+
+      - name: Install SCIMES
+        run: |
+          pip install -r pip-requirements
+          pip install .
+
+      - name: Run tests
+        run: |
+          # use pytest -vv -x for debugging
+          pytest tests

pip-requirements

@@ -2,3 +2,4 @@ astropy>=1.0.2
 matplotlib>=1.4.0
 astrodendro>=0.1.0
 scikit-learn>=0.15.2
+pytest

pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name="SCIMES"
+dynamic = ["version"]
+description="Spectral Clustering for Interstellar Molecular Emission Segmentation"
+readme = "README.md"
+authors = [
+    { name = "Dario Colombo", email = "dario.colombo222@gmail.com"},
+    { name = "Erik Rosolowsky"},
+    { name = "Adam Ginsburg"},
+    { name = "Ana Duarte-Cabral"},
+    { name = "Annie Hughes"},
+]
+maintainers = [
+    { name = "Dario Colombo", email = "dario.colombo222@gmail.com"},
+]
+# license = "BSD"
+# license-files = ["licences/LICENCE.rst"]
+keywords = [
+]
+classifiers=[
+]
+
+requires-python = ">=3.11"
+
+dependencies = [
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "astropy",
+    "scikit-learn",
+    "tqdm",
+    "pytest",
+]
+
+[project.urls]
+Homepage = "http://scimes.readthedocs.org/"
+Repository = "https://github.com/Astroua/SCIMES"
+
+[tool.setuptools.packages.find]
+where = ["src"]

setup.cfg

@@ -7,11 +7,6 @@ all_files = 1
 upload-dir = docs/_build/html
 show-response = 1
 
-[pytest]
-minversion = 2.2
-norecursedirs = build docs/_build
-doctest_plus = enabled
-
 [ah_bootstrap]
 auto_use = True
 
@@ -21,7 +16,7 @@ description = Spectral Clustering for Interstellar Molecular Emission Segmentati
 long_description = Molecular Gas Structure Identification via Dendrogram and Spectral Clustering
 author = Dario Colombo, Erik Rosolowsky, Adam Ginsburg, Ana Duarte-Cabral, and Annie Hughes
 author_email = dario.colombo222@gmail.com
-license = BSD
+# license = BSD
 url = http://scimes.readthedocs.org/
 edit_on_github = True
 github_project = Astroua/SCIMES

scimes/__init__.py → src/scimes/__init__.py

@@ -1,5 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
+from .scimes import *
+
 __version__ = "0.3.2"
 
 """

scimes/plotting.py → src/scimes/plotting.py

@@ -1,4 +1,5 @@
 from matplotlib import pyplot as plt
+import itertools
 
 def dendroplot_clusters(clusters,
                         dend,

scimes/scimes.py → src/scimes/scimes.py

@@ -9,9 +9,11 @@
 from astropy.table import Column
 from sklearn.metrics import silhouette_score
 #from sklearn.manifold import spectral_embedding
-from .old_spectral_embedding import spectral_embedding
+from scimes.old_spectral_embedding import spectral_embedding
 from sklearn.cluster import k_means
 
+__all__ = ['mat_smooth', 'aff_matrix', 'guessk', 'clust_cleaning', 'make_asgncube']  # TODO: complete API
+
 def mat_smooth(Mat, S2Nmat, s2nlim = 3, scalpar = None, lscal = False):
     """
     Estimate the scaling parameter and rescale

tests/dummy_test.py

@@ -0,0 +1,7 @@
+import pytest
+
+def test_dummy():  # pytest automatically calls functions with name starting with test
+    assert True
+
+def test_dummy_failing():
+    assert False

tests/test_installation.py

@@ -0,0 +1,22 @@
+import pytest
+
+def test_import():
+    try:
+        import scimes
+        scimes_importable = True
+    except ImportError:
+        scimes_importable = False
+    assert scimes_importable, 'Cannot import SCIMES at all!'
+
+def test_function_import():
+    # we want to be able to import functions like this
+    from scimes import mat_smooth
+
+    # test for all of them
+    import scimes
+    from scimes.scimes import __all__ as API
+    for name in API:
+        assert getattr(scimes, name) is not None, f'Cannot `from scimes import {name}`'
+
+
+    from scimes.plotting import dendroplot_clusters