Automated Wannierization

.github/workflows/docs.yml

@@ -11,7 +11,7 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: ammaraskar/sphinx-action@master
       with:
         docs-folder: "docs/"

.github/workflows/tests.yml

@@ -18,22 +18,23 @@ jobs:
             os: [ubuntu-latest, macOS-latest]
       steps:
          - name: Checkout
-           uses: actions/checkout@v2
+           uses: actions/checkout@v3
            with:
-              submodules: true
-         - name: Set up Python 3.8
-           uses: actions/setup-python@v2
+              submodules: false
+         - name: Set up Python
+           uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip
               pip install -e .[test]
          - name: Test the source code
            run: |
-              pytest --ci tests/ -m 'not (tutorials or espresso)' --cov-config=.coveragerc --cov=./koopmans/ --cov-report=xml
+              pytest -x --ci tests/ -m 'not (tutorials or espresso)' --cov-config=.coveragerc --cov=./src/koopmans/ --cov-report=xml
          - name: Upload coverage to Codecov
            if: github.repository == 'epfl-theos/koopmans'
-           uses: codecov/codecov-action@v3
+           uses: codecov/codecov-action@v5
            with:
-              file: coverage.xml
+              files: coverage.xml
+              token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tutorials.yml

@@ -18,17 +18,17 @@ jobs:
             os: [ubuntu-latest, macOS-latest]
       steps:
          - name: Checkout
-           uses: actions/checkout@v2
+           uses: actions/checkout@v3
            with:
               submodules: true
-         - name: Set up Python 3.8
-           uses: actions/setup-python@v2
+         - name: Set up Python
+           uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip
               pip install -e .[test]
          - name: Test the tutorials
            run: |
-              pytest --ci tests/ -m tutorials
+              pytest -x --ci tests/ -m tutorials

.github/workflows/typechecking.yml

@@ -16,13 +16,13 @@ jobs:
          max-parallel: 3
       steps:
          - name: Checkout
-           uses: actions/checkout@v2
+           uses: actions/checkout@v3
            with:
               submodules: false
-         - name: Set up Python 3.8
-           uses: actions/setup-python@v2
+         - name: Set up Python
+           uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip

.github/workflows/update_citation.yml

@@ -13,14 +13,14 @@ jobs:
       runs-on: ubuntu-latest
       steps:
          - name: Checkout
-           uses: actions/checkout@v2
+           uses: actions/checkout@v3
          - name: Get branch name
            id: branch-name
-           uses: tj-actions/branch-names@v6
-         - name: Set up Python 3.8
-           uses: actions/setup-python@v2
+           uses: tj-actions/branch-names@v8
+         - name: Set up Python
+           uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip
@@ -30,7 +30,9 @@ jobs:
            run: |
               python bin/update_cff.py
          - name: Validate CITATION.cff
-           uses: dieghernan/cff-validator@main
+           uses: dieghernan/cff-validator@v3
+           with:
+             install-r: true
          - name: Commit changes
            uses: test-room-7/action-update-file@v1
            with:

.gitignore

@@ -6,6 +6,7 @@
 *.pkl
 *.swp
 *.png
+*.log
 __pycache__/
 .vscode
 monkeytype.sqlite3
@@ -17,15 +18,6 @@ coverage.xml
 .mypy_cache/
 TMP-CP/
 TMP/
-calc_alpha/
-calculate_eps/
-dft_bands/
-final/
-init/
-pdos/
-postproc/
-wannier/
-screening/
-hamiltonian/
+??-*/
 build/
 dist/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
         types: [file, python]
@@ -11,19 +11,21 @@ repos:
     -   id: check-yaml
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: src/koopmans/
         args: [--ignore-missing-imports]
+        additional_dependencies:
+          - types-PyYAML
 
   - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.6.0
+    rev: v2.0.4
     hooks:
     - id: autopep8
       args: [--max-line-length=120, -i]

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Specify the python version
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py

CITATION.cff

@@ -1,6 +1,6 @@
 authors:
-- affiliation: École Polytechnique Fédérale de Lausanne
-  email: edward.linscott@epfl.ch
+- affiliation: Paul Scherrer Institut
+  email: edward.linscott@psi.ch
   family-names: Linscott
   given-names: Edward
   orcid: https://orcid.org/0000-0002-4967-9873
@@ -18,7 +18,7 @@ authors:
   given-names: Nicola
   orcid: https://orcid.org/0000-0002-9764-0199
 cff-version: 1.2.0
-license: GPL-3.0
+license: GPL-2.0
 message: If you use this software, please cite it using the metadata from this file.
 preferred-citation:
   authors:
@@ -55,19 +55,20 @@ preferred-citation:
     given-names: Nicola
     orcid: https://orcid.org/0000-0002-9764-0199
   identifiers:
-  - description: DOI of the arXiv preprint
+  - description: DOI of the JCTC article
     type: doi
-    value: 10.48550/arXiv.2302.07759
+    value: 10.1021/acs.jctc.3c00652
   - description: The arXiv preprint
     type: other
-    value: https://arxiv.org/abs/2302.07759
-  journal: arXiv
-  status: preprint
-  title: 'koopmans: an open-source package for accurately and efficiently predicting
-    spectral properties with Koopmans functionals'
+    value: https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00652
+  issue: 20
+  journal: Journal of Chemical Theory and Computation
+  title: 'koopmans: An Open-Source Package for Accurately and Efficiently Predicting
+    Spectral Properties with Koopmans Functionals'
   type: article
+  volume: 19
   year: 2023
 repository-code: https://github.com/epfl-theos/koopmans/
 title: koopmans
 type: software
-version: 1.0.0rc1
+version: 1.1.0