improve packaging

- fix #83
- update metadata
  - use SPDX identifiers for license (and include license files, requires
    setuptools >= 77.0.0 instead of 40ish)
  - replace deprecated codes.open() with open()
- include tests in package; define the pytest "online" tag also in conftest.py
  so that `pytest --pyargs MDAnalysisTests` runs without warnings about undefined
  "online" marker
- avoid warning about MDAnalysis.descr package: include as data (include by looking
  for namespace packages as recommended in https://setuptools.pypa.io/en/latest/userguide/datafiles.html#subdirectory-for-data-files)
- ensure that no stray files (eg __pycache__) from built project are included in package

Author: orbeckst

MANIFEST.in

@@ -1 +1,3 @@
-include README.md AUTHORS LICENSE CHANGELOG.md
+include README.md CHANGELOG.md
+graft MDAnalysisData
+global-exclude __pycache__ *.pyc *~

MDAnalysisData/descr/__init__.py

@@ -0,0 +1,5 @@
+# see also pyproject.toml pytest.markers
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers", "online: will fetch remote files (deselect with with '-m \"not online\"')",
+    )

MDAnalysisData/tests/conftest.py

@@ -1,14 +1,15 @@
 [build-system]
 requires = [
-  "setuptools >= 40.9.0",
+  "setuptools >= 77.0.0",
   "versioningit",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "MDAnalysisData"
 description = "MDAnalysis example data"
-license = {file = "LICENSE" }
+license = "BSD-3-Clause"
+license-files = ["LICENSE", "AUTHORS"]
 authors = [
     {name = "Oliver Beckstein", email = "orbeckst@gmail.com"},
 ]
@@ -19,7 +20,6 @@ classifiers = [
     "Development Status :: 4 - Beta",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "Operating System :: POSIX",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: Microsoft :: Windows ",
@@ -59,17 +59,14 @@ documentation = "https://www.mdanalysis.org/MDAnalysisData"
 
 [tool.setuptools]
 zip-safe = true
-include-package-data = true
 
 [tool.setuptools.packages.find]
-namespaces = false
-include=["MDAnalysisData"]
+namespaces = true
+where = ["."]
 exclude=["docs"]
 
 [tool.setuptools.package-data]
-MDAnalysisData = [
-    "descr/*.rst",
-]
+"MDAnalysisData.descr" = ["*.rst"]
 
 [tool.versioningit]
 default-version = "1+unknown"

pyproject.toml

@@ -1,7 +1,6 @@
 """
 Barebones setup.py for dynamic authors list generation.
 """
-import codecs
 import os
 import warnings
 
@@ -33,7 +32,7 @@ def dynamic_author_list():
     # MDAnalysisData.
 
     authors = []
-    with codecs.open(abspath('AUTHORS'), encoding='utf-8') as infile:
+    with open(abspath('AUTHORS'), encoding='utf-8') as infile:
         # An author is a bullet point under the title "Chronological list of
         # authors". We first want move the cursor down to the title of
         # interest.
@@ -64,7 +63,7 @@ def dynamic_author_list():
 
     # Write the authors.py file.
     out_path = abspath('MDAnalysisData/authors.py')
-    with codecs.open(out_path, 'w', encoding='utf-8') as outfile:
+    with open(out_path, 'w', encoding='utf-8') as outfile:
         # Write the header
         header = '''\
 #-*- coding:utf-8 -*-