Add OpenMM interface

.github/workflows/build-wheels.yml

@@ -111,11 +111,11 @@ jobs:
  matrix:
  torch-version: ['1.12', '1.13', '2.0', '2.1', '2.2', '2.3']
  arch: ['arm64', 'x86_64']
- os: ['ubuntu-22.04', 'macos-11', 'macos-14', 'windows-2019']
+ os: ['ubuntu-22.04', 'macos-13', 'macos-14', 'windows-2019']
  exclude:
  # remove mismatched arch for macOS
  - {os: macos-14, arch: x86_64}
- - {os: macos-11, arch: arm64}
+ - {os: macos-13, arch: arm64}
  # no arm64-windows build
  - {os: windows-2019, arch: arm64}
  # https://github.com/pytorch/pytorch/issues/125109
@@ -124,7 +124,7 @@ jobs:
  - {os: macos-14, arch: arm64, torch-version: '1.12'}
  - {os: macos-14, arch: arm64, torch-version: '1.13'}
  # x86_64-macos is only supported for torch <2.3
- - {os: macos-11, arch: x86_64, torch-version: '2.3'}
+ - {os: macos-13, arch: x86_64, torch-version: '2.3'}
  include:
  # add `cibw-arch` and `rust-target` to the different configurations
  - name: x86_64 Linux
@@ -138,7 +138,7 @@ jobs:
  rust-target: aarch64-unknown-linux-gnu
  cibw-arch: aarch64
  - name: x86_64 macOS
- os: macos-11
+ os: macos-13
  arch: x86_64
  rust-target: x86_64-apple-darwin
  cibw-arch: x86_64
@@ -233,7 +233,7 @@ jobs:
  os: ubuntu-22.04
  arch: arm64
  - name: x86_64 macOS
- os: macos-11
+ os: macos-13
  arch: x86_64
  - name: arm64 macOS
  os: macos-14

docs/generate_examples/conf.py

@@ -2,8 +2,7 @@
 
 import os
 
-from matplotlib.animation import Animation, FFMpegWriter, ImageMagickWriter
-from sphinx_gallery.scrapers import figure_rst, matplotlib_scraper
+from chemiscope.sphinx import ChemiscopeScraper
 from sphinx_gallery.sorting import FileNameSortKey
 
 
@@ -15,56 +14,6 @@
 ROOT = os.path.realpath(os.path.join(HERE, "..", ".."))
 
 
-class AnimationScrapper:
- """
- Alternative image scrapper for sphinx-gallery, rendering the animation to GIF
- instead of a base64-encoded HTML video.
-
- This decreases the size of the documentation and the time taken to render the
- documentation (sphinx-gallery with ``matplotlib_animations=True``) renders the GIF
- and then re-render to create the HTML video.
- """
-
- def __init__(self):
- # only process animations once by storing their `id()` here
- self.seen = set()
-
- def __call__(self, block, block_vars, gallery_conf):
- animations = []
- for variable in block_vars["example_globals"].values():
- if isinstance(variable, Animation) and id(variable) not in self.seen:
- self.seen.add(id(variable))
- animations.append(variable)
-
- if len(animations) == 0:
- # just do the default scrapping
- return matplotlib_scraper(block, block_vars, gallery_conf)
- else:
- # process matplotlib static preview of the animation, and ignore it
- matplotlib_scraper(block, block_vars, gallery_conf)
-
- image_names = []
- for anim, image_path in zip(animations, block_vars["image_path_iterator"]):
- image_path = str(image_path)[:-4] + ".gif"
- image_names.append(image_path)
-
- # this is strongly inspired by the code in sphinx-gallery
- fig_size = anim._fig.get_size_inches()
- thumb_size = gallery_conf["thumbnail_size"]
- use_dpi = round(
- min(t_s / f_s for t_s, f_s in zip(thumb_size, fig_size))
- )
- if FFMpegWriter.isAvailable():
- writer = "ffmpeg"
- elif ImageMagickWriter.isAvailable():
- writer = "imagemagick"
- else:
- writer = None
- anim.save(str(image_path), writer=writer, dpi=use_dpi)
-
- return figure_rst(image_names, gallery_conf["src_dir"])
-
-
 sphinx_gallery_conf = {
  "filename_pattern": ".*",
  "copyfile_regex": r".*\.(example|npz)",
@@ -79,7 +28,7 @@ def __call__(self, block, block_vars, gallery_conf):
  os.path.join(ROOT, "docs", "src", "examples", "atomistic"),
  ],
  "matplotlib_animations": False,
- "image_scrapers": (AnimationScrapper()),
+ "image_scrapers": ("matplotlib", ChemiscopeScraper()),
  "remove_config_comments": True,
  "within_subsection_order": FileNameSortKey,
  "default_thumb_file": os.path.join(