mphowardlab · clpetix · Mar 19, 2025 · Mar 19, 2025 · Mar 19, 2025 · Apr 14, 2025
diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2021-2024, Auburn University
+Copyright (c) 2021-2025, Auburn University
 
 All rights reserved.
 

diff --git a/conftest.py b/conftest.py
@@ -0,0 +1,40 @@
+import numpy
+
+try:
+    import sybil
+    import sybil.parsers.rest
+
+except ImportError:
+    sybil = None
+
+import lammpsio
+
+try:
+    import gsd.hoomd
+
+    has_gsd = True
+except ModuleNotFoundError:
+    has_gsd = False
+
+
+def setup_sybil_tests(namespace):
+    """Sybil setup function."""
+    # Common imports.
+    namespace["numpy"] = numpy
+    namespace["lammpsio"] = lammpsio
+    if has_gsd:
+        namespace["frame"] = gsd.hoomd.Frame()
+    else:
+        namespace["frame"] = 0
+
+
+if sybil is not None:
+    pytest_collect_file = sybil.Sybil(
+        parsers=[
+            sybil.parsers.rest.PythonCodeBlockParser(),
+            sybil.parsers.rest.SkipParser(),
+        ],
+        pattern="*.py",
+        setup=setup_sybil_tests,
+        fixtures=["tmp_path"],
+    ).pytest()
diff --git a/doc/source/api/api reference/lammpsio.Box.rst b/doc/source/api/api reference/lammpsio.Box.rst
@@ -0,0 +1,29 @@
+lammpsio.Box
+============
+
+.. currentmodule:: lammpsio
+
+.. autoclass:: Box
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Box.__init__
+      ~Box.cast
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~Box.high
+      ~Box.low
+      ~Box.tilt
diff --git a/doc/source/api/api reference/lammpsio.DataFile.rst b/doc/source/api/api reference/lammpsio.DataFile.rst
@@ -0,0 +1,31 @@
+lammpsio.DataFile
+=================
+
+.. currentmodule:: lammpsio
+
+.. autoclass:: DataFile
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~DataFile.__init__
+      ~DataFile.create
+      ~DataFile.read
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~DataFile.known_bodies
+      ~DataFile.known_headers
+      ~DataFile.unknown_bodies
+      ~DataFile.unknown_headers
diff --git a/doc/source/api/api reference/lammpsio.DumpFile.rst b/doc/source/api/api reference/lammpsio.DumpFile.rst
@@ -0,0 +1,29 @@
+lammpsio.DumpFile
+=================
+
+.. currentmodule:: lammpsio
+
+.. autoclass:: DumpFile
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~DumpFile.__init__
+      ~DumpFile.create
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~DumpFile.copy_from
+      ~DumpFile.filename
+      ~DumpFile.schema
diff --git a/doc/source/api/api reference/lammpsio.Snapshot.rst b/doc/source/api/api reference/lammpsio.Snapshot.rst
@@ -0,0 +1,56 @@
+lammpsio.Snapshot
+=================
+
+.. currentmodule:: lammpsio
+
+.. autoclass:: Snapshot
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Snapshot.__init__
+      ~Snapshot.from_hoomd_gsd
+      ~Snapshot.has_angles
+      ~Snapshot.has_bonds
+      ~Snapshot.has_charge
+      ~Snapshot.has_dihedrals
+      ~Snapshot.has_id
+      ~Snapshot.has_image
+      ~Snapshot.has_impropers
+      ~Snapshot.has_mass
+      ~Snapshot.has_molecule
+      ~Snapshot.has_position
+      ~Snapshot.has_typeid
+      ~Snapshot.has_velocity
+      ~Snapshot.reorder
+      ~Snapshot.to_hoomd_gsd
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~Snapshot.N
+      ~Snapshot.angles
+      ~Snapshot.bonds
+      ~Snapshot.box
+      ~Snapshot.charge
+      ~Snapshot.dihedrals
+      ~Snapshot.id
+      ~Snapshot.image
+      ~Snapshot.impropers
+      ~Snapshot.mass
+      ~Snapshot.molecule
+      ~Snapshot.num_types
+      ~Snapshot.position
+      ~Snapshot.type_label
+      ~Snapshot.typeid
+      ~Snapshot.velocity
diff --git a/doc/source/api/api reference/lammpsio.topology.rst b/doc/source/api/api reference/lammpsio.topology.rst
@@ -0,0 +1,25 @@
+lammpsio.topology
+=================
+
+.. automodule:: lammpsio.topology
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Angles
+      Bonds
+      Dihedrals
+      Impropers
+      LabelMap
+      Topology
diff --git a/doc/source/api/api.rst b/doc/source/api/api.rst
@@ -0,0 +1,15 @@
+API
+---
+
+Overview
+========
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api reference
-    :toctree: api reference
+    :toctree: generated/
-    :toctree: api reference
+    :toctree: generated/
+
+    lammpsio.Box
+    lammpsio.DataFile
+    lammpsio.DumpFile
+    lammpsio.Snapshot
+    lammpsio.topology
diff --git a/doc/source/api/box.rst b/doc/source/api/box.rst
diff --git a/doc/source/api/data.rst b/doc/source/api/data.rst
diff --git a/doc/source/api/dump.rst b/doc/source/api/dump.rst
diff --git a/doc/source/api/snapshot.rst b/doc/source/api/snapshot.rst
diff --git a/doc/source/api/topology.rst b/doc/source/api/topology.rst
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -13,7 +13,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "lammmpsio"
+project = "lammpsio"
 year = datetime.date.today().year
 copyright = f"2021-{year}, Auburn University"
 author = "Michael P. Howard"

diff --git a/doc/source/guide/credits.rst b/doc/source/guide/credits.rst
@@ -5,4 +5,4 @@ Credits
 * Michael P. Howard
 * Mayukh Kundu
 * Philipp Leclercq
-* C. Levi Petix
+* C\. Levi Petix
diff --git a/doc/source/guide/guidelines.rst b/doc/source/guide/guidelines.rst
@@ -0,0 +1,27 @@
+====================
+Community Guidelines
+====================
+
+We ask that you please review and adhere to our `Code of Conduct`_.
+
+
+Reporting Issues
+================
+If you encounter any bugs or issues while using ``lammpsio``, please report them
+on our `GitHub Issues page`_.
+
+Contributing
+=============
+We welcome contributions to ``lammpsio`` via GitHub pull requests. We ask that
+you please open an issue first to discuss your proposed changes before
+submitting a pull request. This helps us to understand the context of your
+changes and to ensure that they mesh well with the existing codebase.
+
+Seeking Help
+============
+If you have questions or need help using ``lammpsio``, please feel free to reach
+out to us via our `GitHub Discussions page`_.
+
+.. _Code of Conduct: http://github.com/mphowardlab/lammpsio/blob/main/CODE_OF_CONDUCT.md
+.. _GitHub Issues page: http://github.com/mphowardlab/lammpsio/issues
+.. _GitHub Discussions page: http://github.com/mphowardlab/lammpsio/discussions
diff --git a/doc/source/guide/install.rst b/doc/source/guide/install.rst
@@ -8,6 +8,10 @@ The easiest way to get ``lammpsio`` is from PyPI using ``pip``:
 
     pip install lammpsio
 
+or from conda-forge using ``conda`` or ``mamba``:
+.. code:: bash
+
+    conda install -c conda-forge lammpsio
 
 Building from source
 ====================

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -1,25 +1,19 @@
 lammpsio documentation
 ======================
 
-Tools for working with LAMMPS data and dump files.
+lammpsio provides a Python interface for reading and writing LAMMPS
+data and dump files. It also enables interconversion with HOOMD-blue's
+GSD format. This flexible package enables users to work with LAMMPS files
+in a variety of ways that improve workflow efficiency and reproducibility.
 
 
 .. toctree::
     :maxdepth: 1
-    :caption: User guide
 
     guide/install
     guide/examples/index
     guide/release
+    guide/guidelines
     guide/license
     guide/credits
-
-.. toctree::
-    :maxdepth: 1
-    :caption: API reference
-
-    api/box
-    api/data
-    api/dump
-    api/snapshot
-    api/topology
+    api/api.rst