Update docs formatting and requirements

CHANGELOG.rst

@@ -67,11 +67,11 @@ v.2.3.3
 ----------
 - General robustness updates:
  - Updated file parsing to avoid hidden files.
- - Sanity check in `DefectsGenerator` if input symmetry is `P1`.
- - Add `NKRED` to `INCAR` mismatch tests.
+ - Sanity check in ``DefectsGenerator`` if input symmetry is ``P1``.
+ - Add ``NKRED`` to ``INCAR`` mismatch tests.
  - Re-parse config & spin degeneracies in concentration/symmetry functions if data not already present
- (if user is porting `DefectEntry`s from older `doped` versions or manually).
- - Avoid unnecessary `DeprecationWarning`s
+ (if user is porting ``DefectEntry``s from older ``doped`` versions or manually).
+ - Avoid unnecessary ``DeprecationWarning``s
 - Updated docs and linting
 
 v.2.3.2

docs/Tips.rst

@@ -500,10 +500,12 @@ In the typical defect calculation workflow with ``doped`` (exemplified in the tu
  ``DefectsParser(output_path=".")`` – written to ``output_path``. The JSON filename can be set with e.g.
  ``DefectsParser(json_filename="custom_name.json")``, but the default is
  ``{Host Chemical Formula}_defect_dict.json``.
+
  - Additionally, a ``voronoi_nodes.json`` file is saved to the bulk supercell calculation directory if
  any interstitial defects are parsed. This contains information about the Voronoi tessellation nodes
  in the host structure, which are used for analysing interstitial positions but can be somewhat costly
  to calculate – so are automatically saved to file once initially computed to reduce parsing times.
+
 - Additionally, if following the recommended structure-searching approach with ``ShakeNBreak`` as shown in
  the tutorials, ``distortion_metadata.json`` files will be written to the top directory (``output_path``,
  containing distortion information about all defects) and to each defect directory (containing just the

docs/docs_requirements.txt

@@ -1,7 +1,8 @@
-sphinx
-myst-nb
+sphinx>=7
+myst-nb>=1.0
 recommonmark
-renku-sphinx-theme
+renku-sphinx-theme>=0.4.0 # can update to >0.5.0 when https://github.com/SwissDataScienceCenter/renku-sphinx-theme/pull/26 merged
+sphinx_rtd_theme>=1.3.0 # can update to >2.0 when https://github.com/SwissDataScienceCenter/renku-sphinx-theme/pull/26 merged
 sphinx_click
 sphinx_design
 ase
@@ -22,4 +23,4 @@ shakenbreak>=3.3.1
 packaging
 pandas>=1.1.0
 pydefect>=0.8.1
-vise>=0.9.0
+vise>=0.9.0

docs/index.rst

@@ -94,14 +94,14 @@ Studies using ``doped``, so far
 
 - Z\. Yuan & G. Hautier **First-principles study of defects and doping limits in CaO** `Applied Physics Letters <https://doi.org/10.1063/5.0211707>`_ 2024
 - B\. E. Murdock et al. **Li-Site Defects Induce Formation of Li-Rich Impurity Phases: Implications for Charge Distribution and Performance of LiNi** :sub:`0.5-x` **M** :sub:`x` **Mn** :sub:`1.5` **O** :sub:`4` **Cathodes (M = Fe and Mg; x = 0.05–0.2)** `Advanced Materials <https://doi.org/10.1002/adma.202400343>`_ 2024
-- A\. G. Squires et al. **Oxygen dimerization as a defect-driven process in bulk LiNiO₂** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-lcmkj>`_ 2024
+- A\. G. Squires et al. **Oxygen dimerization as a defect-driven process in bulk LiNiO₂** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-lcmkj>`__ 2024
 - Y\. Fu & H. Lohan et al. **Factors Enabling Delocalized Charge-Carriers in Pnictogen-Based Solar Absorbers: In-depth Investigation into CuSbSe<sub>2</sub>** `arXiv <https://doi.org/10.48550/arXiv.2401.02257>`_ 2024
-- S\. Hachmioune et al. **Exploring the Thermoelectric Potential of MgB4: Electronic Band Structure, Transport Properties, and Defect Chemistry** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.4c00584>`_ 2024
-- J\. Hu et al. **Enabling ionic transport in Li3AlP2 the roles of defects and disorder** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-3s0kh>`_ 2024
+- S\. Hachmioune et al. **Exploring the Thermoelectric Potential of MgB4: Electronic Band Structure, Transport Properties, and Defect Chemistry** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.4c00584>`__ 2024
+- J\. Hu et al. **Enabling ionic transport in Li3AlP2 the roles of defects and disorder** `ChemRxiv <https://doi.org/10.26434/chemrxiv-2024-3s0kh>`__ 2024
 - X\. Wang et al. **Upper efficiency limit of Sb₂Se₃ solar cells** `Joule <https://doi.org/10.1016/j.joule.2024.05.004>`_ 2024
-- I\. Mosquera-Lois et al. **Machine-learning structural reconstructions for accelerated point defect calculations** `npj Computational Materials <https://doi.org/10.1038/s41524-024-01303-9>`_ 2024
+- I\. Mosquera-Lois et al. **Machine-learning structural reconstructions for accelerated point defect calculations** `npj Computational Materials <https://doi.org/10.1038/s41524-024-01303-9>`__ 2024
 - W\. Dou et al. **Band Degeneracy and Anisotropy Enhances Thermoelectric Performance from Sb₂Si₂Te₆ to Sc₂Si₂Te₆** `Journal of the American Chemical Society <https://doi.org/10.1021/jacs.4c01838>`_ 2024
-- K\. Li et al. **Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb₂O₅** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.3c03257>`_ 2024
+- K\. Li et al. **Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb₂O₅** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.3c03257>`__ 2024
 - X\. Wang et al. **Four-electron negative-U vacancy defects in antimony selenide** `Physical Review B <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102>`_ 2023
 - Y\. Kumagai et al. **Alkali Mono-Pnictides: A New Class of Photovoltaic Materials by Element Mutation** `PRX Energy <http://dx.doi.org/10.1103/PRXEnergy.2.043002>`__ 2023
 - S\. M. Liga & S. R. Kavanagh, A. Walsh, D. O. Scanlon, G. Konstantatos **Mixed-Cation Vacancy-Ordered Perovskites (Cs₂Ti** :sub:`1–x` **Sn** :sub:`x` **X₆; X = I or Br): Low-Temperature Miscibility, Additivity, and Tunable Stability** `Journal of Physical Chemistry C`_ 2023
@@ -111,7 +111,7 @@ Studies using ``doped``, so far
 - J\. Willis, K. B. Spooner, D. O. Scanlon. **On the possibility of p-type doping in barium stannate** `Applied Physics Letters <https://doi.org/10.1063/5.0170552>`__ 2023
 - J\. Cen et al. **Cation disorder dominates the defect chemistry of high-voltage LiMn** :sub:`1.5` **Ni** :sub:`0.5` **O₄ (LMNO) spinel cathodes** `Journal of Materials Chemistry A`_ 2023
 - J\. Willis & R. Claes et al. **Limits to Hole Mobility and Doping in Copper Iodide** `Chemistry of Materials <https://doi.org/10.1021/acs.chemmater.3c01628>`__ 2023
-- I\. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon **Identifying the ground state structures of point defects in solids** `npj Computational Materials`_ 2023
+- I\. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon **Identifying the ground state structures of point defects in solids** `npj Computational Materials <https://www.nature.com/articles/s41524-023-00973-1>`__ 2023
 - Y\. T. Huang & S. R. Kavanagh et al. **Strong absorption and ultrafast localisation in NaBiS₂ nanocrystals with slow charge-carrier recombination** `Nature Communications`_ 2022
 - S\. R. Kavanagh, D. O. Scanlon, A. Walsh, C. Freysoldt **Impact of metastable defect structures on carrier recombination in solar cells** `Faraday Discussions`_ 2022
 - Y-S\. Choi et al. **Intrinsic Defects and Their Role in the Phase Transition of Na-Ion Anode Na₂Ti₃O₇** `ACS Applied Energy Materials <https://doi.org/10.1021/acsaem.2c03466>`__ 2022
@@ -129,7 +129,6 @@ Studies using ``doped``, so far
 
 .. _Journal of Physical Chemistry C: https://doi.org/10.1021/acs.jpcc.3c05204
 .. _Journal of Materials Chemistry A: https://doi.org/10.1039/D3TA00532A
-.. _npj Computational Materials: https://www.nature.com/articles/s41524-023-00973-1
 .. _Nature Communications: https://www.nature.com/articles/s41467-022-32669-3
 .. _Faraday Discussions: https://doi.org/10.1039/D2FD00043A
 .. _Chemical Science: https://doi.org/10.1039/D1SC03775G

doped/utils/plotting.py

@@ -157,7 +157,7 @@ def format_defect_name(
  Format defect name for plot titles.
 
  (i.e. from Cd_i_C3v_0 to $Cd_{i}^{0}$ or $Cd_{i_{C3v}}^{0}$).
- Note this assumes "V_" means vacancy not Vanadium.
+ Note this assumes "V_..." means vacancy not Vanadium.
 
  Args:
  defect_species (:obj:`str`):