Switch to a pyproject.toml (#163)

* initial tomlification attempt

* fix completeness

* fix completeness for real

* use correct length

* update buiild workflow

* fix dynamic versioning

---------

Co-authored-by: Kevin Dalton <[email protected]>

.github/workflows/build.yml

@@ -33,11 +33,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .[dev]
     
     - name: Test with pytest
       run: |
-        python setup.py test
+        pytest
     
     - name: Upload coverage to Codecov  
       uses: codecov/codecov-action@v3

.github/workflows/publish.yml

@@ -16,12 +16,12 @@ jobs:
         python-version: '3.10'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install packaging setuptools twine wheel
+        python -m pip install --upgrade pip build
+        python -m pip install packaging setuptools twine wheel
     - name: Publish the Python package
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*

careless/stats/completeness.py

@@ -31,26 +31,30 @@ def __init__(self):
 def run_analysis(args):
     ds = rs.read_mtz(args.mtz)
     results = rs.stats.compute_completeness(ds, bins=args.bins)
+    results = results['completeness']
 
-    if args.output is not None:
-        results.to_csv(args.output)
-    else:
-        print(results.to_string())
 
     #Move overall to the beginning
     results = results.iloc[np.roll(np.arange(len(results)), 1)]
+    results = results.reset_index()
+    xlabel = 'Resolution Range (Å)'
+    results = results.rename(columns={'index' : xlabel})
+
+    if args.output is not None:
+        results.to_csv(args.output, index=False)
+    else:
+        print(results.to_string(index=False))
 
     ax = sns.lineplot(
-        data=results.reset_index().melt('index'),
-        x='index',
+        data=results.reset_index().melt(xlabel),
+        x=xlabel,
         y='value',
-        hue='variable_1',
+        hue='variable',
         palette='Dark2',
     )
     plt.xticks(rotation=45, rotation_mode='anchor', ha='right')
     plt.legend(title="")
     plt.ylabel(r"Completeness")
-    plt.xlabel("Resolution ($\mathrm{\AA}$)")
     plt.grid(which='both', axis='both', ls='dashdot')
     plt.tight_layout()
 

pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "careless"
+authors=[
+    {name="Kevin M. Dalton", email="[email protected]"}
+]
+description = "Merging crystallography data without much physics."
+readme = "README.md"
+dynamic = ["version"]
+requires-python = ">= 3.9,<3.12"
+dependencies = [
+    "reciprocalspaceship>=0.9.16",
+    "tqdm",
+    "tensorflow",
+    "tf_keras",
+    "tensorflow-probability[tf]",
+    "matplotlib",
+    "seaborn",
+    "ray",
+]
+optional-dependencies.dev = [
+    "pytest", 
+    "pytest-cov",
+    "pytest-xdist",
+]
+license={text = "MIT"}
+
+[project.urls]
+Repository = "https://github.com/rs-station/careless"
+Examples = "https://github.com/rs-station/careless-examples"
+Issues = "https://github.com/rs-station/careless/issues"
+
+[project.scripts]
+careless = "careless.careless:main"
+"careless.ccanom" = "careless.stats.ccanom:main"
+"careless.cchalf" = "careless.stats.cchalf:main"
+"careless.ccpred" = "careless.stats.ccpred:main"
+"careless.image_ccpred" = "careless.stats.image_cc:main"
+"careless.filter_image" = "careless.stats.filter_by_image_cc:main"
+"careless.plot_history" = "careless.stats.history:main"
+"careless.bfactor" = "careless.stats.prior_b:main"
+"careless.apply_bfactor" = "careless.stats.rescale:main"
+"careless.completeness" = "careless.stats.completeness:main"
+"careless.rsplit" = "careless.stats.rsplit:main"
+"careless.xds2mtz" = "careless.io.xds:main"
+
+[tool.pytest.ini_options]
+addopts = "-n auto --cov=careless --cov-config=.coveragerc --cov-report xml"
+testpaths = [
+    "tests",
+]
+
+[tool.setuptools.dynamic]
+version = {file = "careless/VERSION"}

tests/stats/test_completeness.py

@@ -23,5 +23,6 @@ def test_completeness(merged_mtz, bins):
     assert exists(png)
 
     df = pd.read_csv(csv)
-    assert len(df) == bins + 2
+
+    assert len(df) == bins + 1