Add functional style methods to HasStructure

[pmrv]

This adds some transform/filter methods to HasStructure to allow a "functional programming" style in its use. Contingent on #853 and some tests/docs.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[coveralls]

Pull Request Test Coverage Report for Build 3622667903

• 17 of 28 (60.71%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.008%) to 68.654%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/atomistics/job/atomistic.py	0	1	0.0%
pyiron_atomistics/atomistics/structure/has_structure.py	15	25	60.0%

Totals
Change from base Build 3622625190:	-0.008%
Covered Lines:	12116
Relevant Lines:	17648

---

💛 - Coveralls

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[liamhuber]

lgtm

[liamhuber]

The rest of the CI needs to be triggered, but now that this isn't a draft, I bet the black formatting commit will trigger it.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jan-janssen]

It seems like this pull request broke the documentation jobs.

[pmrv]

Since both #921 and #920 also fail docs, I'm not sure if this one is the cause. I'll see if I can reproduce the issue locally.

[jan-janssen]

Since both #921 and #920 also fail docs, I'm not sure if this one is the cause. I'll see if I can reproduce the issue locally.

Yes, I agree ... still it is a bit frustrating that it is unrelated as it makes debugging even more complicated.

[pmrv]

Here's the full error log from sphinx

# Platform:         linux; (Linux-6.1.1-arch1-1-x86_64-with-glibc2.36)
# Sphinx version:   6.1.1
# Python version:   3.11.0 (CPython)
# Docutils version: 0.19
# Jinja2 version:   3.1.2
# Pygments version: 2.14.0

# Last messages:
#   reading sources... [ 91%] apidoc/pyiron_atomistics.yaff.yaff
#   reading sources... [ 91%] index
#   reading sources... [ 92%] source/about
#   reading sources... [ 92%] source/examples
#   reading sources... [ 92%] source/faq
#   reading sources... [ 93%] source/import
#   reading sources... [ 93%] source/indices
#   reading sources... [ 93%] source/installation
#   reading sources... [ 94%] source/notebooks/QHA
#   reading sources... [ 94%] source/notebooks/Thermodynamics_QHA

# Loaded extensions:
#   sphinx.ext.mathjax (6.1.1)
#   sphinxcontrib.applehelp (1.0.2)
#   sphinxcontrib.devhelp (1.0.2)
#   sphinxcontrib.htmlhelp (2.0.0)
#   sphinxcontrib.serializinghtml (1.1.5)
#   sphinxcontrib.qthelp (1.0.3)
#   alabaster (0.7.12)
#   nbsphinx (0.8.11)
#   sphinx.ext.autodoc.preserve_defaults (6.1.1)
#   sphinx.ext.autodoc.type_comment (6.1.1)
#   sphinx.ext.autodoc.typehints (6.1.1)
#   sphinx.ext.autodoc (6.1.1)
#   sphinx.ext.viewcode (6.1.1)
#   sphinx.ext.autosummary (6.1.1)
#   sphinx.ext.napoleon (6.1.1)

# Traceback:
Traceback (most recent call last):
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/cmd/build.py", line 284, in build_main
    app.build(args.force_all, args.filenames)
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/application.py", line 347, in build
    self.builder.build_update()
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 311, in build_update
    self.build(to_build,
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 327, in build
    updated_docnames = set(self.read())
                           ^^^^^^^^^^^
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 434, in read
    self._read_serial(docnames)
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 455, in _read_serial
    self.read_doc(docname)
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 511, in read_doc
    publisher.publish()
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/docutils/core.py", line 226, in publish
    self.apply_transforms()
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/docutils/core.py", line 206, in apply_transforms
    self.document.transformer.apply_transforms()
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/transforms/__init__.py", line 80, in apply_transforms
    super().apply_transforms()
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/docutils/transforms/__init__.py", line 173, in apply_transforms
    transform.apply(**kwargs)
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/transforms/__init__.py", line 206, in apply
    apply_source_workaround(node)
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/util/nodes.py", line 175, in apply_source_workaround
    node.source = get_node_source(node) or ''
                  ^^^^^^^^^^^^^^^^^^^^^
  File "/home/ponder/micromamba/envs/pyiron_atomistics_docs/lib/python3.11/site-packages/sphinx/util/nodes.py", line 273, in get_node_source
    raise ValueError("node source not found")
ValueError: node source not found

It sounds like that's actually an issue with them.