Merge pull request #74 from SMTG-Bham/develop

Develop

.github/workflows/pip_install_test.yml

@@ -40,6 +40,7 @@ jobs:
           sleep 360  # wait 10 minutes for PyPI to update with the new release
           python -m pip install --upgrade pip
           pip install doped[tests]  # install only from PyPI
+          pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF  # avoid spglib warnings
 
       - name: Test
         run: |

.github/workflows/test.yml

@@ -34,6 +34,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e .[tests]
+          pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF  # avoid spglib warnings
 
       - name: Test
         run:  |

CHANGELOG.rst

@@ -1,6 +1,10 @@
 Change Log
 ==========
 
+v.2.4.3
+----------
+- Remove ``spglib<=2.0.2`` dependency (set to avoid unnecessary warnings), and update installation instructions accordingly.
+
 v.2.4.2
 ----------
 - Allow cases where the calculated host material is unstable wrt competing phases (above the hull), by downshifting to the hull and warning the user about this.

README.md

@@ -31,8 +31,14 @@ displacements from DFT supercell calculations. See the [JOSS paper](https://doi.
 ## Installation
 ```bash
 pip install doped  # install doped and dependencies
+conda install -c conda-forge spglib  # bundle C libraries with spglib
 ```
 
+Note that either `conda install -c conda-forge spglib` or
+`pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF`
+should be used after `pip install doped`, which ensures that the correct C libraries are bundled with
+`spglib`, to prevent unnecessary warnings.
+
 Alternatively if desired, `doped` can also be installed from `conda` with:
 
 ```bash

docs/Installation.rst

@@ -6,6 +6,19 @@ Installation
 .. code-block:: bash
 
    pip install doped  # install doped and dependencies
+   conda install -c conda-forge spglib  # bundle C libraries with spglib
+
+Note that either ``conda install -c conda-forge spglib`` or
+``pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF``
+should be used after ``pip install doped``, which ensures that the correct C libraries are bundled with
+``spglib``, to prevent unnecessary warnings. You can check that the correct C libraries have been bundled
+by running the following in Python, and confirming that the same version numbers are printed:
+
+.. code-block:: python
+
+   import spglib
+   print(spglib.__version__)
+   print(spglib.spg_get_version_full())
 
 Alternatively if desired, ``doped`` can also be installed from ``conda`` with:
 

docs/Troubleshooting.rst

@@ -65,7 +65,7 @@ that it is rebuilt with the new ``numpy`` C API:
 
 ``spglib`` Errors/Warnings
 --------------------------
-A previous known issue with ``spglib`` is that it could give an error or warnings similar to:
+A known issue with ``spglib`` is that it can give unnecessary errors or warnings similar to:
 
 .. code:: python
 
@@ -76,20 +76,12 @@ A previous known issue with ``spglib`` is that it could give an error or warning
   spglib: get_bravais_exact_positions_and_lattice failed
   spglib: ref_get_exact_structure_and_symmetry failed.
 
-This can be fixed by reinstalling ``spglib`` with ``conda install -c conda-forge spglib==2.0.2``.
-Sometimes installation with ``conda`` rather than ``pip`` is required, as ``conda``  will bundle the C
-and Fortran libraries, while using version ``2.0.2`` for now avoids some unnecessary warnings (see this
-`Issue <https://github.com/spglib/spglib/issues/338>`_ on the ``spglib`` GitHub for details).
+This can be fixed by reinstalling ``spglib`` with ``conda install -c conda-forge spglib`` or
+``pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF``
+as detailed in the `Installation <https://doped.readthedocs.io/en/latest/Installation.html>`__ instructions.
+This ensures the correct C libraries are bundled with ``spglib``.
 
-.. If this still does not remove these warnings, then setting the environment variable: ``SPGLIB_WARNING=OFF``
-and re-installing ``spglib`` with:
-
-.. .. code:: bash
-
-..   pip uninstall spglib
-  pip install git+https://github.com/spglib/spglib --config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF
-
-.. should fix it. – STILL DOESN'T FULLY FIX IT YET (see doped_spglib_warnings.ipynb)
+.. see doped_spglib_warnings.ipynb
 
 ``ShakeNBreak``
 -------------------

docs/conf.py

@@ -25,7 +25,7 @@
 author = 'Seán R. Kavanagh'
 
 # The full version, including alpha/beta/rc tags
-release = '2.4.2'
+release = '2.4.3'
 
 
 # -- General configuration ---------------------------------------------------

doped/utils/symmetry.py

@@ -27,6 +27,38 @@
 )
 
 
+def _set_spglib_warnings_env_var():
+    """
+    Set the SPGLIB environment variable to suppress spglib warnings.
+    """
+    os.environ["SPGLIB_WARNING"] = "OFF"
+
+
+def _check_spglib_version():
+    """
+    Check the versions of spglib and its C libraries, and raise a warning if
+    the correct installation instructions have not been followed.
+    """
+    import spglib
+
+    python_version = spglib.__version__
+    c_version = spglib.spg_get_version_full()
+
+    if python_version != c_version:
+        warnings.warn(
+            f"Your spglib Python version (spglib.__version__ = {python_version}) does not match its C "
+            f"library version (spglib.spg_get_version_full() = {c_version}). This can lead to unnecessary "
+            f"spglib warning messages, but can be avoided by installing spglib with `conda install -c "
+            f"conda-forge spglib` or `pip install git+https://github.com/spglib/spglib "
+            f"--config-settings=cmake.define.SPGLIB_SHARED_LIBS=OFF` as detailed in the doped "
+            f"installation instructions: https://doped.readthedocs.io/en/latest/Installation.html"
+        )
+
+
+_check_spglib_version()
+_set_spglib_warnings_env_var()
+
+
 def _round_floats(obj, places=5):
     """
     Recursively round floats in a dictionary to ``places`` decimal places.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "doped"
-version = "2.4.2"
+version = "2.4.3"
 description = "Python package to setup, process and analyse solid-state defect calculations with VASP"
 authors = [{name = "Seán Kavanagh", email = "skavanagh@seas.harvard.edu"}]
 readme = "README.md"
@@ -22,8 +22,11 @@ dependencies = [
     "matplotlib>=3.5.2",
     "numpy>=1.21.0",
     "pymatgen>=2023.11.12",  # limiting factor: POTCAR_STATS_PATH available from pymatgen.io.vasp.inputs
-    "spglib<=2.0.2",  # dependent of pymatgen, but explicitly set to <=2.0.2 here to avoid unnecessary warnings
-    # see https://github.com/spglib/spglib/issues/338; remove this limit when issue resolved
+    "spglib>=2.4.0",  # previously explicitly set to <=2.0.2 to avoid unnecessary warnings
+    # (https://github.com/spglib/spglib/issues/338) but causing dependency issues
+    # (https://github.com/SMTG-Bham/doped/issues/73), being worked on in
+    # https://github.com/spglib/spglib/issues/462 -- update Troubleshooting.rst and spglib warning in
+    # doped.utils.symmetry when finally resolved
     "pymatgen-analysis-defects>=2023.8.22",
     "shakenbreak>=3.3.1",
     "pandas",