Migrate PEP517 backend to Hatchling

Hatch/Hatchling (https://hatch.pypa.io/) Uses standard pyproject.toml
[project] table settings, like setuptools, but provides more places
for extensibility. That's used here to automatically generate the
`dxtbx.format` and `console_scripts` entry-points on build.

A change was needed because pip had started raising "pending removal"
noises about the way we deployed before.

Opportunity take to do some more pyproject.toml consolidations.

dependencies.yaml

@@ -85,7 +85,7 @@ run:
 test:
   - dials-data
   - pip
-  - pytest
+  - pytest >6
   - pytest-mock
   - pytest-nunit # [win]
   - pytest-xdist

hatch_build.py

@@ -0,0 +1,98 @@
+"""
+Dynamically generate the list of console_scripts dxtbx.format entry-points.
+"""
+
+from __future__ import annotations
+
+import ast
+import re
+from pathlib import Path
+
+from hatchling.metadata.plugin.interface import MetadataHookInterface
+
+
+def get_entry_point(
+    filename: Path, prefix: str, import_path: str
+) -> list[tuple[str, str]]:
+    """Returns any entry point strings for a given path.
+
+    This looks for LIBTBX_SET_DISPATCHER_NAME, and a root function
+    named 'run'. It can return multiple results for each file, if more
+    than one dispatcher name is bound.
+
+    Args:
+        filename:
+            The python file to parse. Will look for a run() function
+            and any number of LIBTBX_SET_DISPATCHER_NAME.
+        prefix: The prefix to output the entry point console script with
+        import_path: The import path to get to the package the file is in
+
+    Returns:
+        A list of entry_point specifications
+    """
+    contents = filename.read_text()
+    tree = ast.parse(contents)
+    # Find root functions named "run"
+    has_run = any(
+        x
+        for x in tree.body
+        if (isinstance(x, ast.FunctionDef) and x.name == "run")
+        or (isinstance(x, ast.ImportFrom) and "run" in [a.name for a in x.names])
+    )
+    if not has_run:
+        return []
+    # Find if we need an alternate name via LIBTBX_SET_DISPATCHER_NAME
+    alternate_names = re.findall(
+        r"^#\s*LIBTBX_SET_DISPATCHER_NAME\s+(.*)$", contents, re.M
+    )
+    if alternate_names:
+        return [
+            (name, f"{import_path}.{filename.stem}:run") for name in alternate_names
+        ]
+
+    return [(f"{prefix}.{filename.stem}", f"{import_path}.{filename.stem}:run")]
+
+
+def enumerate_format_classes(path: Path) -> list[tuple(str, str)]:
+    """Find all Format*.py files and contained Format classes in a path"""
+    format_classes = []
+    for filename in path.glob("Format*.py"):
+        content = filename.read_bytes()
+        try:
+            parsetree = ast.parse(content)
+        except SyntaxError:
+            print(f"  *** Could not parse {filename.name}")
+            continue
+        for top_level_def in parsetree.body:
+            if not isinstance(top_level_def, ast.ClassDef):
+                continue
+            base_names = [
+                baseclass.id
+                for baseclass in top_level_def.bases
+                if isinstance(baseclass, ast.Name) and baseclass.id.startswith("Format")
+            ]
+            if base_names:
+                classname = top_level_def.name
+                format_classes.append(
+                    (
+                        f"{classname}:{','.join(base_names)}",
+                        f"dxtbx.format.{filename.stem}:{classname}",
+                    )
+                )
+    return format_classes
+
+
+class CustomMetadataHook(MetadataHookInterface):
+    def update(self, metadata):
+        scripts = metadata.setdefault("scripts", {})
+        package_path = Path(self.root) / "src" / "dxtbx"
+        for file in package_path.joinpath("command_line").glob("*.py"):
+            for name, symbol in get_entry_point(file, "dxtbx", "dxtbx.command_line"):
+                if name not in scripts:
+                    scripts[name] = symbol
+
+        plugins = metadata.setdefault("entry-points", {})
+        formats = plugins.setdefault("dxtbx.format", {})
+        for name, symbol in sorted(enumerate_format_classes(package_path / "format")):
+            if name not in formats:
+                formats[name] = symbol

newsfragments/XXX.misc

@@ -0,0 +1 @@
+Switch build backend to hatchling. This lets us avoid deprecated setuptools behaviour, and automatically generate metadata in a more future-proof way.

pyproject.toml

@@ -1,5 +1,34 @@
-[tool.black]
-include = '\.pyi?$|/SConscript$|/libtbx_config$'
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "dxtbx"
+version = "3.23.dev"
+description = "Diffraction Experiment Toolkit"
+authors = [
+    { name = "Diamond Light Source", email = "[email protected]" },
+]
+license = { file = "LICENSE.txt" }
+readme = "README.md"
+requires-python = ">=3.9, <3.13"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+]
+dynamic = ["entry-points", "scripts"]
+
+[project.urls]
+Homepage = "https://dials.github.io"
+Repository = "https://github.com/cctbx/dxtbx"
+
+[tool.hatch.metadata.hooks.custom.entry-points]
 
 [tool.towncrier]
 package = "dxtbx"
@@ -67,3 +96,12 @@ section-order = [
 
 [tool.mypy]
 no_implicit_optional = true
+
+[tool.pytest.ini_options]
+addopts = "-rsxX"
+filterwarnings = [
+    "ignore:the matrix subclass is not the recommended way:PendingDeprecationWarning",
+    "ignore:numpy.dtype size changed:RuntimeWarning",
+    "ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning",
+    "ignore:`product` is deprecated as of NumPy:DeprecationWarning:h5py|numpy",
+]