libAtoms · jameskermode · Jul 6, 2023 · Feb 10, 2023 · Feb 10, 2023 · Feb 10, 2023
diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
@@ -25,7 +25,7 @@ jobs:
       matrix:
         buildplat:
         - [ubuntu-20.04, manylinux, x86_64]
-        - [macos-10.15, macosx, x86_64]
+        - [macos-12, macosx, x86_64]
         - [windows-2019, win, AMD64]
 
         python: ["cp38", "cp39", "cp310", "cp311"]

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -20,7 +20,9 @@ jobs:
       - name: install_python
         run: |
           sudo apt-get update -qy
-          sudo apt-get install -y python3-dev python3-pip libxml2-dev libxslt-dev zlib1g-dev meson
+          sudo apt-get install -y python3-dev python3-pip libxml2-dev libxslt-dev zlib1g-dev
+          # Upgrade to latest meson and ninja
+          sudo pip install --upgrade meson ninja
 
       - name: install_package
         run: |

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -23,7 +23,9 @@ jobs:
       - name: install_python
         run: |
           sudo apt-get update -qy
-          sudo apt-get install -y python3-dev python3-pip python3-venv libxml2-dev libxslt-dev zlib1g-dev meson
+          sudo apt-get install -y python3-dev python3-pip python3-venv libxml2-dev libxslt-dev zlib1g-dev
+          # Upgrade to latest meson and ninja
+          sudo pip install --upgrade meson ninja
 
       - name: build_c
         run: |

diff --git a/ChangeLog.md b/ChangeLog.md
@@ -9,6 +9,9 @@ v0.8.0 (not yet released)
 - Writing and reading inhomogenous (and non numeric) data with savetbl/readtbl
 - Hessian-based preconditioner
 - Changed build system to Meson
+- Removed `contact_mechanics` submodule. Stable alternatives:
+  [ContactMechanics](https://github.com/ContactEngineering/ContactMechanics) or
+  [Tamaas](https://gitlab.com/tamaas/tamaas)
 
 v0.7.0 (29Jul21)
 ----------------

diff --git a/docs/api/calculators.rst b/docs/api/calculators.rst
@@ -0,0 +1,4 @@
+Calculators
+-----------
+
+.. automodule:: matscipy.calculators
diff --git a/docs/api/dislocation.rst b/docs/api/dislocation.rst
@@ -0,0 +1,4 @@
+Dislocation
+----------
+
+.. automodule:: matscipy.dislocation
diff --git a/docs/api/elasticity.rst b/docs/api/elasticity.rst
@@ -0,0 +1,4 @@
+Elasticity
+----------
+
+.. automodule:: matscipy.elasticity
diff --git a/docs/api/fracture_mechanics.rst b/docs/api/fracture_mechanics.rst
@@ -0,0 +1,4 @@
+Fracture Mechanics
+------------------
+
+.. automodule:: matscipy.fracture_mechanics
diff --git a/docs/api/neighbours.rst b/docs/api/neighbours.rst
@@ -0,0 +1,4 @@
+Neighbour lists
+---------------
+
+.. automodule:: matscipy.neighbours
diff --git a/docs/api/numerical.rst b/docs/api/numerical.rst
@@ -0,0 +1,4 @@
+Numerical
+---------
+
+.. automodule:: matscipy.numerical
diff --git a/docs/api/root.rst b/docs/api/root.rst
@@ -0,0 +1,4 @@
+Matscipy root
+-------------
+
+.. automodule:: matscipy
diff --git a/docs/api_reference.rst b/docs/api_reference.rst
@@ -0,0 +1,11 @@
+API Reference
+=============
+
+.. toctree::
+   ./api/root
+   ./api/calculators
+   ./api/elasticity
+   ./api/neighbours
+   ./api/numerical
+   ./api/fracture_mechanics
+   ./api/dislocation
diff --git a/docs/calculators.rst b/docs/calculators.rst
@@ -0,0 +1,5 @@
+Calculators
+===========
+
+Here's a description of the calculators available in `matscipy` and how they can
+be composed.
diff --git a/docs/conf.py b/docs/conf.py
@@ -26,8 +26,9 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../'))
+
+# sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('../'))
 
 # -- General configuration ------------------------------------------------
 
@@ -269,3 +270,14 @@
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
+
+# -- Extension configuration -------------------------------------------------
+
+autodoc_default_options = {
+    'members': True,
+    'member-order': 'bysource',
+    'undoc-members': True,
+    'show-inheritance': True,
+    'inherited-members': True,
+    'special-members': '__init__',
+}
diff --git a/docs/elastic_constants.rst b/docs/elastic_constants.rst
@@ -0,0 +1,4 @@
+Elastic Constants
+=================
+
+Here's how to use `matscipy` to evaluate elastic constants of an RVE.
diff --git a/docs/fracture_mechanics.rst b/docs/fracture_mechanics.rst
@@ -0,0 +1,4 @@
+Fracture Mechanics
+==================
+
+Here's what you can do with Matscipy in the field of fracture mechanics.
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,37 +6,49 @@
 .. include:: ../README.rst
 
 
-Contents
-========
-
-.. autosummary::
-
-   matscipy.angle_distribution
-   matscipy.atomic_strain
-   matscipy.calculators
-   matscipy.calculators.eam
-   matscipy.calculators.pair_potential
-   matscipy.calculators.mcfm
-   matscipy.calculators.supercell_calculator
-   matscipy.calculators.manybody
-   matscipy.contact_mechanics
-   matscipy.contact_mechanics.DMT
-   matscipy.contact_mechanics.greens_function
-   matscipy.contact_mechanics.Hertz
-   matscipy.contact_mechanics.JKR
-   matscipy.elasticity
-   matscipy.fracture_mechanics
-   matscipy.fracture_mechanics.clusters
-   matscipy.fracture_mechanics.crack
-   matscipy.fracture_mechanics.crackpathsel
-   matscipy.fracture_mechanics.energy_release
-   matscipy.fracture_mechanics.idealbrittlesolid
-   matscipy.hydrogenate
-   matscipy.io
-   matscipy.logger
-   matscipy.neighbours
-   matscipy.rings
-   matscipy.surface
+..
+   Matscipy submodules
+   ===================
+
+   .. autosummary::
+
+      matscipy.angle_distribution
+      matscipy.atomic_strain
+      matscipy.calculators
+      matscipy.calculators.eam
+      matscipy.calculators.pair_potential
+      matscipy.calculators.mcfm
+      matscipy.calculators.supercell_calculator
+      matscipy.calculators.manybody
+      matscipy.contact_mechanics
+      matscipy.contact_mechanics.DMT
+      matscipy.contact_mechanics.greens_function
+      matscipy.contact_mechanics.Hertz
+      matscipy.contact_mechanics.JKR
+      matscipy.elasticity
+      matscipy.fracture_mechanics
+      matscipy.fracture_mechanics.clusters
+      matscipy.fracture_mechanics.crack
+      matscipy.fracture_mechanics.crackpathsel
+      matscipy.fracture_mechanics.energy_release
+      matscipy.fracture_mechanics.idealbrittlesolid
+      matscipy.hydrogenate
+      matscipy.io
+      matscipy.logger
+      matscipy.neighbours
+      matscipy.numerical
+      matscipy.rings
+      matscipy.surface
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Table of Contents:
+
+   ./calculators
+   ./fracture_mechanics
+   ./plasticity
+   ./elastic_constants
+   ./api_reference
 
 
 Indices and tables

diff --git a/docs/plasticity.rst b/docs/plasticity.rst
@@ -0,0 +1,4 @@
+Plasticity
+==========
+
+Here's what you can do with Matscipy in the field of plasticity.
diff --git a/matscipy/calculators/committee/__init__.py b/matscipy/calculators/committee/__init__.py
@@ -0,0 +1,5 @@
+"""Implements the Committee (of Models) approach."""
+
+from .committee import CommitteeUncertainty, Committee, CommitteeMember
+from .log import set_logging
+from .utils import subsample