website restructured; plot.particles and plot.fields type hint corrected

amepproject · Oct 22, 2024 · 03ff184 · 03ff184
1 parent b901ad2
commit 03ff184
Show file tree

Hide file tree

Showing 12 changed files with 26 additions and 519 deletions.
diff --git a/README.md b/README.md
@@ -185,7 +185,7 @@ simulation data.
 
 
 | Observable | Particles | Fields |
-|:----------:|:---------:|:------:|
+|:-----------|:---------:|:------:|
 | **Spatial Correlation Functions:** |||
 | RDF (radial pair distribution function) | ✔ | ➖ |
 | PCF2d (2d pair correlation function) | ✔ | ➖ |

diff --git a/amep/load.py b/amep/load.py
@@ -33,7 +33,7 @@
 import os
 import h5py
 
-from .reader import LammpsReader, H5amepReader, ContinuumReader, GSDReader
+from .reader import LammpsReader, H5amepReader, ContinuumReader
 from .trajectory import ParticleTrajectory,FieldTrajectory
 from .base import TRAJFILENAME, BaseEvalData, BaseDatabase, LOADMODES
 from .base import check_path, get_module_logger
@@ -226,16 +226,7 @@ def traj(
             **kwargs
         )
         return FieldTrajectory(reader)
-    elif mode == 'gsd':
-        reader = GSDReader(
-            directory,
-            savedir,
-            trajfile = trajfile,
-            deleteold = deleteold,
-            verbose = verbose,
-            **kwargs
-        )
-        return ParticleTrajectory(reader)
+
     # here one has to check both the amep version with which the file has been
     # created (reader.version) and the data type (particles or fields) -
     # the latter is needed to decide whether a ParticleTrajectory or a

diff --git a/amep/plot.py b/amep/plot.py
@@ -909,7 +909,7 @@ def box(axis: mpl.axes.Axes, box_boundary: np.ndarray, **kwargs) -> None:
 
 
 def particles(
-        ax: mpl.axes, coords: np.ndarray, box_boundary: np.ndarray,
+        ax: mpl.axes.Axes, coords: np.ndarray, box_boundary: np.ndarray,
         radius: np.ndarray | float, scalefactor: float = 1.0,
         values: np.ndarray | None = None,
         cmap: list | str = 'viridis', set_ax_limits: bool = True,
@@ -1081,7 +1081,7 @@ def particles(
 
 
 def field(
-        ax: mpl.axes, density: np.ndarray, X: np.ndarray, Y: np.ndarray,
+        ax: mpl.axes.Axes, density: np.ndarray, X: np.ndarray, Y: np.ndarray,
         cmap: list | str = 'plasma', box_boundary: np.ndarray | None = None,
         vmin: float | None = None, vmax: float | None = None,
         cscale: str = 'lin', verbose: bool = False, **kwargs

diff --git a/amep/reader.py b/amep/reader.py
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -9,7 +9,7 @@
 project = 'AMEP'
 copyright = '2023-2024, Lukas Hecht, Kay-Robert Dormann, Kai Luca Spanheimer'
 author = 'Lukas Hecht, Kay-Robert Dormann, Kai Luca Spanheimer'
-release = '1.0.2'
+release = '1.0.3'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -51,7 +51,7 @@
                 "url": "https://github.com/amepproject/amep",  # required
                 # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
                 "icon": "fa-brands fa-square-github",
-                # The type of image to be used (see below for details)
+                # The type of image to be used
                 "type": "fontawesome",
             },
             {
@@ -61,8 +61,16 @@
                 "url": "https://pypi.org/project/amep/",  # required
                 # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
                 "icon": "fa-brands fa-python",
-                # The type of image to be used (see below for details)
+                # The type of image to be used
                 "type": "fontawesome",
             }
-            ]
-        }
+        ],
+        #"switcher": {
+        #    "json_url": "https://amepproject.de/switcher.json",
+        #    "version_match": release
+        #},
+        #"check_switcher": True,
+        #"navbar_persistent": ["search-button.html", "theme-switcher.html"],
+        #"navbar_end": ["version-switcher.html", "icon-links.html"]
+        # "navbar_start": ["navbar_logo", "version-switcher"]
+    }
diff --git a/doc/source/datastructures/particle_data_reader.md b/doc/source/datastructures/particle_data_reader.md
diff --git a/doc/source/user_guide/howto_cite.rst → doc/source/howto_cite.rst b/doc/source/user_guide/howto_cite.rst → doc/source/howto_cite.rst
@@ -1,6 +1,6 @@
-=====================
-How to cite **AMEP**
-=====================
+============
+How to Cite
+============
 
 If you use **AMEP** for a project that leads to a scientific publication, please acknowledge 
 the use of **AMEP** within the body of your publication for example by copying or adapting 

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -3,8 +3,8 @@
   :align: center
 
 
-AMEP documentation
-==================
+AMEP 1.0.3 documentation
+========================
 
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
@@ -17,7 +17,7 @@ Table of Contents
    :maxdepth: 2
 
    gettingstarted/index
-   datastructures/index
+   howto_cite
    user_guide/index
    api
 

diff --git a/doc/source/datastructures/field_data.rst → .../user_guide/datastructures/field_data.rst b/doc/source/datastructures/field_data.rst → .../user_guide/datastructures/field_data.rst
diff --git a/doc/source/datastructures/function_flow.rst → ...er_guide/datastructures/function_flow.rst b/doc/source/datastructures/function_flow.rst → ...er_guide/datastructures/function_flow.rst
diff --git a/doc/source/datastructures/index.rst → ...ource/user_guide/datastructures/index.rst b/doc/source/datastructures/index.rst → ...ource/user_guide/datastructures/index.rst
@@ -11,7 +11,3 @@ the sections below.
 .. toctree::
 
    field_data
-
-.. toctree::
-
-    particle_data_reader
diff --git a/doc/source/user_guide/index.rst b/doc/source/user_guide/index.rst
@@ -15,7 +15,7 @@ your research.
 
 .. toctree::
 
-   howto_cite
+   datastructures/index
 
 .. toctree::