Merge pull request #208 from libAtoms/24_joss_response

MAINT: Addressing JOSS review reports
libAtoms · Jan 5, 2024 · a4101ae · a4101ae
2 parents af3305e + 12f780c
commit a4101ae
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diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -28,7 +28,7 @@ jobs:
         - [macos-12, macosx, x86_64]
         - [windows-2019, win, AMD64]
 
-        python: ["cp38", "cp39", "cp310", "cp311"]
+        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
       fail-fast: false
 
     env:
@@ -44,7 +44,7 @@ jobs:
           python-version: '3.8'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.3
+        uses: pypa/cibuildwheel@v2.16.2
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}

diff --git a/README.rst b/README.rst
@@ -1,3 +1,5 @@
+|Tests| |Wheels|
+
 Matscipy
 ========
 
@@ -65,6 +67,28 @@ To run the tests locally, from Matscipy's root directory::
   cd tests/
   python3 -m pytest .
 
+Editable installs
+~~~~~~~~~~~~~~~~~
+
+When developing `matscipy`, it can be useful to have an editable install of
+the source directory. This means that changes to the source code are directly
+reflected in the `matscipy` install. We are using *Meson* and *meson-python* as a
+build system, and there are some `restriction to editable installs <https://meson-python.readthedocs.io/en/latest/how-to-guides/editable-installs.html>`__.
+
+The editable install only works with the
+`--no-build-isolation` option::
+
+  python3 -m pip install --no-build-isolation --editable .[test]
+
+If you get the message::
+
+  ERROR: Tried to form an absolute path to a dir in the source tree.
+
+then you are most likely try to install into a Python virtual environment that
+is located inside your source directory. This is not possible; your virtual
+environment needs to be located outside of the source directory.
+
+
 Dependencies
 ------------
 
@@ -85,3 +109,8 @@ Funding
 
 **matscipy** was partially funded by the Deutsch Forschungsgemeinschaft (project `258153560 <https://gepris.dfg.de/gepris/projekt/258153560>`__) and by the Engineering and Physical Sciences Research Council (grants `EP/P002188/1 <https://gow.epsrc.ukri.org/NGBOViewGrant.aspx?GrantRef=EP/P002188/1>`__, `EP/R012474/1 <https://gow.epsrc.ukri.org/NGBOViewGrant.aspx?GrantRef=EP/R012474/1>`__ and `EP/R043612/1 <https://gow.epsrc.ukri.org/NGBOViewGrant.aspx?GrantRef=EP/R043612/1>`__).
 
+.. |Tests| image:: https://github.com/libAtoms/matscipy/actions/workflows/tests.yml/badge.svg
+   :target: https://github.com/libAtoms/matscipy/actions/workflows/tests.yml
+
+.. |Wheels| image:: https://github.com/libAtoms/matscipy/actions/workflows/wheels.yml/badge.svg
+   :target: https://github.com/libAtoms/matscipy/actions/workflows/wheels.yml
diff --git a/c/angle_distribution.cpp b/c/angle_distribution.cpp
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/angle_distribution.h b/c/angle_distribution.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/islands.cpp b/c/islands.cpp
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/islands.h b/c/islands.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/matscipymodule.c b/c/matscipymodule.c
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/matscipymodule.h b/c/matscipymodule.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/neighbours.c b/c/neighbours.c
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/neighbours.h b/c/neighbours.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/ring_statistics.cpp b/c/ring_statistics.cpp
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/ring_statistics.h b/c/ring_statistics.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/stack.h b/c/stack.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/test_stack.cpp b/c/test_stack.cpp
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/tools.c b/c/tools.c
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/c/tools.h b/c/tools.h
@@ -1,7 +1,5 @@
 /* ======================================================================
    matscipy - Python materials science tools
-   https://github.com/pastewka/atomistica
-
    https://github.com/libAtoms/matscipy
 
    Copyright (2014) James Kermode, King's College London

diff --git a/docs/tools/angle_distribution.ipynb b/docs/tools/angle_distribution.ipynb
diff --git a/docs/tools/index.rst b/docs/tools/index.rst
@@ -7,5 +7,6 @@ Analysis tools
 
    neighbour_list
    pair_distribution
+   angle_distribution
    ring_analysis
    setup_non-reactive_simulations
diff --git a/docs/tools/pair_distribution.ipynb b/docs/tools/pair_distribution.ipynb
diff --git a/env.sh b/env.sh