Update and consolidate tests and docs CI

.github/workflows/JOSS_draft-PDF.yaml

@@ -1,20 +1,24 @@
-on: [push]
+on:
+  workflow_dispatch:  # only if manually run or on main branch
+
+  push:
+    branches: [ main ]
 
 jobs:
   paper:
     runs-on: ubuntu-latest
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           # This should be the path to the paper within your repo.
           paper-path: docs/JOSS/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v5
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/pip_install_test.yml

@@ -18,15 +18,20 @@ jobs:
       fail-fast: false
 
       matrix:
+        os: [ ubuntu-latest, macos-14 ]
         python-version: [ '3.9', '3.10', '3.11' ]
-        os: [ ubuntu-latest ]
+        exclude:
+          - os: macos-14
+            python-version: '3.9'  # Exclude Python 3.9 on macOS, not supported for macOS-14 tests
+        # macos-latest should be 14 according to link below, but currently doesn't?
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
 
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -55,7 +60,7 @@ jobs:
       # Upload test plots
       - name: Archive test plots
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: output-plots
           path: tests/remote_baseline

.github/workflows/release.yml

@@ -16,11 +16,11 @@ jobs:
     # only run when tests have passed (or manually triggered)
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |

.github/workflows/test.yml

@@ -3,9 +3,6 @@ name: Tests
 on:
   workflow_dispatch:
 
-  pull_request:
-    branches:
-       - '*'  # all branches
   push:
     branches:
       - '*'  # all branches
@@ -16,15 +13,20 @@ jobs:
       fail-fast: false
 
       matrix:
+        os: [ ubuntu-latest, macos-14 ]
         python-version: [ '3.9', '3.10', '3.11' ]
-        os: [ ubuntu-latest ]
+        exclude:
+          - os: macos-14
+            python-version: '3.9'  # Exclude Python 3.9 on macOS, not supported for macOS-14 tests
+        # macos-latest should be 14 according to link below, but currently doesn't?
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
 
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -52,7 +54,7 @@ jobs:
       # Upload test plots
       - name: Archive test plots
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: output-plots
           path: tests/remote_baseline

.readthedocs.yaml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Build from the docs/ directory with Sphinx
 sphinx:

docs/Dev_ToDo.md

@@ -91,4 +91,5 @@
 - Deal with cases where "X-rich"/"X-poor" corresponds to more than one limit (pick one and warn user?)
 - `dist_tol` should also group defects for the concentration etc functions, currently doesn't (e.g. `CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)` and `CdTe_thermo.dist_tol=10; CdTe_thermo.get_equilibrium_concentrations(limit="Te-rich", per_charge=False, fermi_level=0.5)`, same output)
 - Add example to chemical potentials / thermodynamics analysis tutorials of varying chemical potentials as a function of temperature/pressure (i.e. gas phases), using the `Spinney` functions detailed here (https://spinney.readthedocs.io/en/latest/tutorial/chemipots.html#including-temperature-and-pressure-effects-through-the-gas-phase-chemical-potentials) or possibly `DefAP` functions otherwise.
-- Plotting lines colour updates.
+- Plotting lines colour updates.
+- Archive/delete `paper` branch

doped/utils/legacy_corrections.py

@@ -44,7 +44,7 @@ def get_murphy_image_charge_correction(
         verbose (bool): If True details of the correction will be printed.
 
     Returns:
-        The image charge correction as {charge: correction}
+        The image charge correction as a ``{charge: correction}`` dictionary.
     """
     inv_diel = np.linalg.inv(dielectric_matrix)
     det_diel = np.linalg.det(dielectric_matrix)