fix: make changes for conda-forge compatibility (#200)

* fix: use matplotlib-base when installing with conda-forge

* refactor: rename cli entrypoint to 'snmf' from 'diffpy.stretched-nmf'

* chore: add news item for previous commit

* fix: produce an error if test files are missing

* docs: explain the current entrypoint when the help command is used

---------

Co-authored-by: John Halloran <jhalloran@oxy.edu>

Author: john-halloran

README.rst

@@ -69,6 +69,10 @@ The preferred method is conda::
         conda create -n diffpy.stretched-nmf_env diffpy.stretched-nmf
         conda activate diffpy.stretched-nmf_env
 
+For interactive plotting with ``show_plots=True``, use a GUI-capable desktop
+environment. Conda installs use ``matplotlib-base``, which is sufficient for
+plotting but still depends on an available interactive Matplotlib backend.
+
 Alternatively, install from PyPI with pip::
 
         pip install diffpy.stretched-nmf
@@ -79,13 +83,13 @@ For source installs (after cloning the repo)::
 
 Quick check::
 
-        diffpy.stretched-nmf --version
+        snmf --version
         python -c "import diffpy.stretched_nmf; print(diffpy.stretched_nmf.__version__)"
 
 
 To view the basic usage and available commands, type ::
 
-        diffpy.stretched-nmf -h
+        snmf -h
 
 Getting Started
 ---------------

docs/source/getting-started.rst

@@ -17,6 +17,10 @@ The preferred method is conda:
    conda create -n diffpy.stretched-nmf_env diffpy.stretched-nmf
    conda activate diffpy.stretched-nmf_env
 
+For interactive plotting with ``show_plots=True``, use a GUI-capable desktop
+environment. Conda installs use ``matplotlib-base``, which is sufficient for
+plotting but still depends on an available interactive Matplotlib backend.
+
 Alternatively, install from PyPI with pip:
 
 .. code-block:: bash
@@ -36,7 +40,7 @@ Verify the CLI and Python import:
 
 .. code-block:: bash
 
-   diffpy.stretched-nmf --version
+   snmf --version
    python -c "import diffpy.stretched_nmf; print(diffpy.stretched_nmf.__version__)"
 
 Basic usage

news/forge-cleanup.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Rename cli entrypoint to 'snmf' from 'diffpy.stretched-nmf'
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Produce an error if test files are missing
+* Use matplotlib-base when installing with conda-forge
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -49,7 +49,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-"diffpy.stretched-nmf" = "diffpy.stretched_nmf.snmf_app:main"
+"snmf" = "diffpy.stretched_nmf.snmf_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

requirements/conda.txt

@@ -1,5 +1,5 @@
 numpy
-matplotlib
+matplotlib-base
 scipy
 cvxpy
 diffpy.utils

src/diffpy/stretched_nmf/snmf_app.py

@@ -5,9 +5,12 @@
 
 def main():
     parser = argparse.ArgumentParser(
-        prog="diffpy.stretched-nmf",
+        prog="snmf",
         description=(
             "A python package implementing the stretched NMF algorithm.\n\n"
+            "Currently, this project is used by importing "
+            "`SNMFOptimizer` in Python rather than through a command-line "
+            "workflow.\n\n"
             "For more information, visit: "
             "https://github.com/diffpy/diffpy.stretched-nmf/"
         ),
@@ -23,7 +26,7 @@ def main():
     args = parser.parse_args()
 
     if args.version:
-        print(f"diffpy.stretched-nmf {__version__}")
+        print(f"snmf {__version__}")
     else:
         # Default behavior when no arguments are given
         parser.print_help()

tests/test_snmf_optimizer.py

@@ -5,28 +5,33 @@
 
 from diffpy.stretched_nmf.snmf_class import SNMFOptimizer
 
-DATA_DIR = Path(__file__).parent / "inputs/test_snmf_optimizer"
+DATA_DIR = (
+    Path(__file__).resolve().parents[1]
+    / "docs/examples/data/XRD-MgMnO-YCl-real"
+)
 
-# Skip the test entirely if any inputs file is missing
 _required = [
     "init-components.txt",
     "source-matrix.txt",
     "init-stretch.txt",
     "init-weights.txt",
 ]
 _missing = [f for f in _required if not (DATA_DIR / f).exists()]
-pytestmark = pytest.mark.skipif(
-    _missing, reason=f"Missing test data files: {_missing}"
-)
 
 
 @pytest.fixture(scope="module")
 def inputs():
+    if _missing:
+        pytest.fail(
+            f"Missing required test data files in {DATA_DIR}: {_missing}"
+        )
     return {
         "components": np.loadtxt(
             DATA_DIR / "init-components.txt", dtype=float
         ),
-        "source": np.loadtxt(DATA_DIR / "source-matrix.txt", dtype=float),
+        "source": np.loadtxt(
+            DATA_DIR / "source-matrix.txt", dtype=float, skiprows=4
+        ),
         "stretch": np.loadtxt(DATA_DIR / "init-stretch.txt", dtype=float),
         "weights": np.loadtxt(DATA_DIR / "init-weights.txt", dtype=float),
     }