WIP, BLD: meson, spin support

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -52,3 +52,11 @@ benchmarks/results
 .idea
 .vscode
 *.lock
+!pixi.lock
+
+# meson
+.wraplock
+build-install
+# pixi environments
+.pixi/*
+!.pixi/config.toml

package/.spin/cmds.py

@@ -0,0 +1,9 @@
+import spin
+
+
+@spin.util.extend_command(spin.cmds.meson.test, doc="")
+def test(*, parent_callback, pytest_args, tests, coverage,
+         **kwargs):
+    pytest_args = ('MDAnalysisTests',) + pytest_args
+    parent_callback(**{"pytest_args": pytest_args, "tests": tests,
+                    "coverage": coverage, **kwargs})

package/MDAnalysis/analysis/data/meson.build

@@ -0,0 +1,8 @@
+py3.install_sources([
+    '__init__.py',
+    'janin_ref_data.npy',
+    'rama_ref_data.npy',
+    'filenames.py',
+  ],
+  subdir: 'MDAnalysis/analysis/data'
+)

package/MDAnalysis/analysis/dssp/meson.build

@@ -0,0 +1,7 @@
+py3.install_sources([
+    '__init__.py',
+    'dssp.py',
+    'pydssp_numpy.py',
+  ],
+  subdir: 'MDAnalysis/analysis/dssp'
+)

package/MDAnalysis/analysis/encore/clustering/meson.build

@@ -0,0 +1,21 @@
+affinityprop_src = ['src/ap.c']
+
+py3.extension_module('affinityprop',
+  affinityprop_src + [cython_gen.process('affinityprop.pyx')],
+  cpp_args: cython_c_args,
+  include_directories: [
+    'include',
+    ],
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/analysis/encore/clustering'
+)
+
+py3.install_sources([
+    'ClusterCollection.py',
+    'ClusteringMethod.py',
+    '__init__.py',
+    'cluster.py',
+  ],
+  subdir: 'MDAnalysis/analysis/encore/clustering'
+)

package/MDAnalysis/analysis/encore/dimensionality_reduction/meson.build

@@ -0,0 +1,21 @@
+affinityprop_src = ['src/spe.c']
+
+py3.extension_module('stochasticproxembed',
+  affinityprop_src + [cython_gen.process('stochasticproxembed.pyx')],
+  c_args: cython_c_args,
+  include_directories: [
+    'include',
+    ],
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/analysis/encore/dimensionality_reduction'
+)
+
+py3.install_sources([
+'DimensionalityReductionMethod.py',
+'__init__.py',
+'reduce_dimensionality.py',
+  ],
+  subdir: 'MDAnalysis/analysis/encore/dimensionality_reduction'
+)
+

package/MDAnalysis/analysis/encore/meson.build

@@ -0,0 +1,21 @@
+py3.extension_module('cutils',
+  [cython_gen_cpp.process('cutils.pyx')],
+  cpp_args: cython_cpp_args,
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/analysis/encore'
+)
+
+py3.install_sources([
+'__init__.py',
+'bootstrap.py',
+'confdistmatrix.py',
+'covariance.py',
+'similarity.py',
+'utils.py',
+  ],
+  subdir: 'MDAnalysis/analysis/encore'
+)
+
+subdir('clustering')
+subdir('dimensionality_reduction')

package/MDAnalysis/analysis/hbonds/meson.build

@@ -0,0 +1,7 @@
+py3.install_sources([
+'__init__.py',
+'hbond_autocorrel.py',
+  ],
+  subdir: 'MDAnalysis/analysis/hbonds'
+)
+

package/MDAnalysis/analysis/hole2/meson.build

@@ -0,0 +1,5 @@
+py3.install_sources([
+    '__init__.py',
+  ],
+  subdir: 'MDAnalysis/analysis/hole2'
+)

package/MDAnalysis/analysis/hydrogenbonds/meson.build

@@ -0,0 +1,9 @@
+py3.install_sources([
+    '__init__.py',
+    'hbond_autocorrel.py',
+    'wbridge_analysis.py',
+    'hbond_analysis.py',
+  ],
+  subdir: 'MDAnalysis/analysis/hydrogenbonds'
+)
+

package/MDAnalysis/analysis/meson.build

@@ -0,0 +1,37 @@
+py3.install_sources([
+'__init__.py',
+'backends.py',
+'bat.py',
+'contacts.py',
+'density.py',
+'dielectric.py',
+'dihedrals.py',
+'distances.py',
+'helix_analysis.py',
+'leaflet.py',
+'nucleicacids.py',
+'nuclinfo.py',
+'pca.py',
+'results.py',
+'rms.py',
+'gnm.py',
+'lineardensity.py',
+'psa.py',
+'waterdynamics.py',
+'base.py',
+'rdf.py',
+'align.py',
+'atomicdistances.py',
+'diffusionmap.py',
+'msd.py',
+'polymer.py',
+  ],
+  subdir: 'MDAnalysis/analysis'
+)
+
+subdir('data')
+subdir('dssp')
+subdir('hydrogenbonds')
+subdir('encore')
+subdir('hole2')
+subdir('hbonds')

package/MDAnalysis/auxiliary/meson.build

@@ -0,0 +1,9 @@
+py3.install_sources([
+    '__init__.py',
+    'base.py', 
+    'core.py',
+    'EDR.py',
+    'XVG.py',
+  ],
+  subdir: 'MDAnalysis/auxiliary'
+)

package/MDAnalysis/converters/meson.build

@@ -0,0 +1,14 @@
+py3.install_sources([
+    'OpenMM.py',
+    'OpenMMParser.py',
+    'ParmEdParser.py',
+    'base.py',
+    'ParmEd.py',
+    'RDKit.py',
+    'RDKitInferring.py',
+    'RDKitParser.py',
+    '__init__.py',
+  ],
+  subdir: 'MDAnalysis/converters'
+)
+

package/MDAnalysis/coordinates/meson.build

@@ -0,0 +1,47 @@
+py3.extension_module('timestep',
+  [cython_gen_cpp.process('timestep.pyx')],
+  cpp_args: cython_cpp_args,
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/coordinates'
+)
+
+py3.install_sources([
+    'CRD.py',
+    'DMS.py',
+    'FHIAIMS.py',
+    'NAMDBIN.py',
+    'ParmEd.py',
+    'TNG.py',
+    'core.py',
+    'null.py',
+    'DLPoly.py',
+    'GRO.py',
+    'GSD.py',
+    'INPCRD.py',
+    'MMTF.py',
+    'PDBQT.py',
+    'PQR.py',
+    'TRJ.py',
+    'TRZ.py',
+    'XDR.py',
+    'TRC.py',
+    'base.py',
+    'DCD.py',
+    'GMS.py',
+    'H5MD.py',
+    'LAMMPS.py',
+    'MOL2.py',
+    'PDB.py',
+    'TPR.py',
+    'TRR.py',
+    'TXYZ.py',
+    'XTC.py',
+    'XYZ.py',
+    '__init__.py',
+    'chain.py',
+    'chemfiles.py',
+    'memory.py',
+  ],
+  subdir: 'MDAnalysis/coordinates'
+)

package/MDAnalysis/core/meson.build

@@ -0,0 +1,14 @@
+py3.install_sources([
+    '__init__.py',
+    '_get_readers.py',
+    'accessors.py',
+    'groups.py',
+    'topology.py',
+    'topologyattrs.py',
+    'topologyobjects.py',
+    'selection.py',
+    'universe.py',
+  ],
+  subdir: 'MDAnalysis/core'
+)
+

package/MDAnalysis/guesser/meson.build

@@ -0,0 +1,9 @@
+py3.install_sources([
+    '__init__.py',
+    'tables.py',
+    'base.py',
+    'default_guesser.py',
+  ],
+  subdir: 'MDAnalysis/guesser'
+)
+

package/MDAnalysis/lib/formats/meson.build

@@ -0,0 +1,46 @@
+py3.extension_module('cython_util',
+  [cython_gen_cpp.process('cython_util.pyx')],
+  cpp_args: cython_cpp_args,
+  include_directories: [
+    'include',
+    ],
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/lib/formats'
+)
+
+py3.extension_module('libdcd',
+  [cython_gen_cpp.process('libdcd.pyx')],
+  cpp_args: cython_cpp_args,
+  include_directories: [
+    'include',
+    ],
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/lib/formats'
+)
+
+xdr_src = [
+    'src/xdrfile_trr.c',
+    'src/xdrfile_xtc.c',
+    'src/xdrfile.c',
+    'src/trr_seek.c',
+    'src/xtc_seek.c',
+]
+
+py3.extension_module('libmdaxdr',
+  xdr_src + [cython_gen_cpp.process('libmdaxdr.pyx')],
+  cpp_args: cython_cpp_args,
+  include_directories: [
+    'include',
+    ],
+  dependencies: np_dep,
+  install: true,
+  subdir: 'MDAnalysis/lib/formats'
+)
+
+py3.install_sources([
+    '__init__.py',
+  ],
+  subdir: 'MDAnalysis/lib/formats'
+)