Updated docs.

.github/workflows/test.yml

@@ -6,7 +6,7 @@ name: test
 
 on:
   push:
-    branches: [ "main", "2.1.0", "optimization"]
+    branches: [ "main"]
   pull_request:
     branches: [ "main"]
 

docs/docs/reference/geometry.md

@@ -220,42 +220,6 @@ is within the half-closed interval [0, 1)
 By wrapping values near 1 to 0 we will have a consistent way of
 presenting systems.
 
-## get\_displacement\_tensor\_old
-
-```python
-def get_displacement_tensor_old(pos1,
-                                pos2,
-                                cell=None,
-                                pbc=None,
-                                mic=False,
-                                cutoff=None,
-                                return_factors=False,
-                                return_distances=False)
-```
-
-Given an array of positions, calculates the 3D displacement tensor
-between the positions.
-
-The displacement tensor is a matrix where the entry A[i, j, :] is the
-vector pos1[i] - pos2[j], i.e. the vector from pos2 to pos1
-
-**Arguments**:
-
-- `pos1(np.ndarray)` - 2D array of positions
-- `pos2(np.ndarray)` - 2D array of positions
-- `cell(np.ndarray)` - Cell for taking into account the periodicity
-  pbc(boolean or a list of booleans): Periodicity of the axes
-- `mic(boolean)` - Whether to return the displacement to the nearest
-  periodic copy
-
-
-**Returns**:
-
-- `np.ndarray` - 3D displacement tensor
-  (optional) np.ndarray: The indices of the periodic copies in which the
-  minimum image was found
-  (optional) np.ndarray: The lengths of the displacement vectors
-
 ## find\_mic
 
 ```python
@@ -398,7 +362,7 @@ Also takes periodic boundaries into account.
 ## get\_matches
 
 ```python
-def get_matches(system, positions, numbers, tolerances, mic=True)
+def get_matches(system, cell_list, positions, numbers, tolerance)
 ```
 
 Given a system and a list of cartesian positions and atomic numbers,
@@ -408,10 +372,10 @@ positions with some tolerance.
 **Arguments**:
 
 - `system(ASE.Atoms)` - System where to search the positions
+- `cell_list(CellList)` - The cell list for an appropriately extended version
+  of the system.
 - `positions(np.ndarray)` - Positions to match in the system.
-- `tolerances(np.ndarray)` - Maximum allowed distance for each vector that
-  is allowed for a match in position.
-- `mic(boolean)` - Whether to find the minimum image copy.
+- `tolerance(float)` - Maximum allowed distance for matching.
 
 
 **Returns**:
@@ -422,10 +386,10 @@ positions with some tolerance.
 - `np.ndarray` - for each searched position, an integer array representing
   the number of the periodic copy where the match was found.
 
-## get\_matches\_new
+## get\_matches\_simple
 
 ```python
-def get_matches_new(system, cell_list, positions, numbers, tolerances)
+def get_matches_simple(system, cell_list, positions, numbers, tolerance)
 ```
 
 Given a system and a list of cartesian positions and atomic numbers,
@@ -438,29 +402,26 @@ positions with some tolerance.
 - `cell_list(CellList)` - The cell list for an appropriately extended version
   of the system.
 - `positions(np.ndarray)` - Positions to match in the system.
-- `tolerances(np.ndarray)` - Maximum allowed distance for each vector that
-  is allowed for a match in position.
-
+- `tolerance(float)` - Maximum allowed distance for matching.
 
 **Returns**:
 
-- `np.ndarray` - indices of matched atoms
-- `list` - list of substitutions
-- `list` - list of vacancies
-- `np.ndarray` - for each searched position, an integer array representing
-  the number of the periodic copy where the match was found.
+- `list` - list of matched atoms or None is nothing was matched.
 
 ## get\_cell\_list
 
 ```python
-def get_cell_list(positions, indices, factors, cutoff=0)
+def get_cell_list(positions, cell, pbc, extension, cutoff)
 ```
 
 Given a system and a cutoff value, returns a cell list object.
 
 **Arguments**:
 
-- `system(ASE.Atoms)` - System to extend
+- `positions(np.ndarray)` - Cartesian positions
+- `cell(np.ndarray)` - Cell as 3x3 array
+- `pbc(np.ndarray)` - Periodic boundary conditions as array of three booleans
+- `extension(float)` - How much the system should be extended for the search.
 - `cutoff(float)` - Radial cutoff
 
 

docs/docs/reference/sbc.md

@@ -12,16 +12,6 @@ periodically repeating motifs, and as such it is not suitable for e.g.
 finding molecules. Any atoms that do not have enough periodic repetitions
 will be returned as isolated clusters.
 
-## \_\_init\_\_
-
-```python
-def __init__(seed=7)
-```
-
-**Arguments**:
-
-- `seed(int)` - The seed that is used for random number generation.
-
 ## get\_clusters
 
 ```python
@@ -33,7 +23,8 @@ def get_clusters(system,
                  merge_radius=1,
                  bond_threshold=0.65,
                  overlap_threshold=-0.1,
-                 radii="covalent")
+                 radii="covalent",
+                 seed=7)
 ```
 
 Used to detect and return structurally separate clusters within the
@@ -67,6 +58,7 @@ given system.
   - vdw: van Der Waals radii from DOI:10.1039/C3DT50599E
   - vdw_covalent: preferably van Der Waals radii, covalent if vdw
   not defined.
+- `seed(int)` - The seed that is used for random number generation.
 
 
 **Returns**:

docs/package.json

@@ -14,9 +14,9 @@
     "write-heading-ids": "docusaurus write-heading-ids"
   },
   "dependencies": {
-    "@docusaurus/core": "^3.1.1",
-    "@docusaurus/plugin-ideal-image": "^3.1.1",
-    "@docusaurus/preset-classic": "^3.1.1",
+    "@docusaurus/core": "^3.4.0",
+    "@docusaurus/plugin-ideal-image": "^3.4.0",
+    "@docusaurus/preset-classic": "^3.4.0",
     "@mdx-js/react": "^3.0.0",
     "clsx": "^1.2.1",
     "hast-util-is-element": "^1.1.0",
@@ -28,8 +28,8 @@
     "remark-math": "^6.0.0"
   },
   "devDependencies": {
-    "@docusaurus/module-type-aliases": "^3.1.1",
-    "@docusaurus/types": "^3.1.1"
+    "@docusaurus/module-type-aliases": "^3.4.0",
+    "@docusaurus/types": "^3.4.0"
   },
   "browserslist": {
     "production": [

docs/pydoc-markdown.yml

@@ -1,5 +1,6 @@
 loaders:
   - type: python
+    search_path: [../]
 processors:
   - type: filter
     skip_empty_modules: true