Merge branch 'develop' into publish-gh-pages

phonopy · Jun 29, 2024 · a5be390 · a5be390
2 parents c49bdb1 + 6ae8b66
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diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         conda install --yes python=${{ matrix.python-version }}
         #conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         conda install --yes python=${{ matrix.python-version }}
         #conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-mkl.yml b/.github/workflows/phono3py-pytest-conda-mkl.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         conda install --yes python=${{ matrix.python-version }}
         #conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-numpy2.yml b/.github/workflows/phono3py-pytest-conda-numpy2.yml
@@ -0,0 +1,59 @@
+name: Pytest with openblas and numpy 2.0
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+    - name: Install dependent packages
+      run: |
+        conda activate test
+        conda install --yes python=${{ matrix.python-version }}
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest codecov pytest-cov cmake c-compiler
+    - name: Install spglib develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/spglib/spglib.git
+        cd spglib
+        pip install -e . -vvv
+        cd ..
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
+    - name: Install phonopy develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        cd phonopy
+        PHONOPY_USE_OPENMP=true pip install -e . -vvv
+        cd ..
+    - name: Install phono3py
+      run: |
+        conda activate test
+        pip install -e . -vvv
+    - name: Run pytest
+      run: |
+        pytest -v test
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        verbose: true
diff --git a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         conda install --yes python=${{ matrix.python-version }}
         conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
         #conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

diff --git a/.github/workflows/publish-gh-pages.yml b/.github/workflows/publish-gh-pages.yml
@@ -15,8 +15,8 @@ jobs:
         python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml
@@ -17,9 +17,9 @@ jobs:
         python-version: ["3.10", ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,31 +10,12 @@ repos:
     exclude: ^conda/
   - id: check-added-large-files
 
-- repo: https://github.com/pycqa/flake8
-  rev: 7.0.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.10
   hooks:
-  - id: flake8
-    args:
-    - "--max-line-length=88"
-    - "--ignore=E203,W503"
-
-- repo: https://github.com/psf/black
-  rev: 24.4.2
-  hooks:
-  - id: black
-    args:
-    - --line-length=88
-
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.3.0
-  hooks:
-  - id: pydocstyle
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-      name: isort (python)
+  - id: ruff
+    args: [ "--fix", "--show-fixes" ]
+  - id: ruff-format
 
 - repo: https://github.com/Takishima/cmake-pre-commit-hooks
   rev: v1.9.6

diff --git a/README.md b/README.md
@@ -6,41 +6,40 @@
 
 # phono3py
 
-A simulation package of phonon-phonon interaction related properties. Phono3py
-user documentation is found at http://phonopy.github.io/phono3py/.
+A simulation package of phonon-phonon interaction related properties mainly
+written in python. Phono3py user documentation is found at
+http://phonopy.github.io/phono3py/.
 
 ## Mailing list for questions
 
 Usual phono3py questions should be sent to phonopy mailing list
 (https://sourceforge.net/p/phonopy/mailman/).
 
+## Dependency
+
+See `requirements.txt`. Optionally `symfc` and `scipy` are required
+for using additional features.
+
 ## Development
 
 The development of phono3py is managed on the `develop` branch of github
 phono3py repository.
 
 - Github issues is the place to discuss about phono3py issues.
 - Github pull request is the place to request merging source code.
-- Python 3.7 is the minimum requirement.
-- Formatting is written in `pyproject.toml`.
-- Not strictly, but VSCode's `settings.json` may be written like
+- Formatting rules are found in `pyproject.toml`.
+- Not strictly, but VSCode's `settings.json` may be written like below
 
   ```json
-  "python.linting.flake8Enabled": true,
-  "python.linting.flake8Args": ["--max-line-length=88", "--ignore=E203,W503"],
-  "python.linting.enabled": true,
-  "python.linting.pylintEnabled": false,
-  "python.linting.mypyEnabled": true,
-  "python.linting.pycodestyleEnabled": false,
-  "python.linting.pydocstyleEnabled": true,
-  "python.formatting.provider": "black",
-  "python.formatting.blackArgs": ["--line-length=88"],
-  "python.sortImports.args": ["--profile", "black"],
+  "ruff.lint.args": [
+      "--config=${workspaceFolder}/pyproject.toml",
+  ],
   "[python]": {
+      "editor.defaultFormatter": "charliermarsh.ruff",
       "editor.codeActionsOnSave": {
-      "source.organizeImports": true
-    },
-  }
+          "source.organizeImports": "explicit"
+      }
+  },
   ```
 
 - Use of pre-commit (https://pre-commit.com/) is encouraged.
@@ -57,7 +56,8 @@ stored in `doc` directory. Please see how to write the documentation at
 
 ## How to run tests
 
-You need pytest. At home directory of phono3py after setup,
+Tests are written using pytest. To run tests, pytest has to be installed. The
+tests can be run by
 
 ```bash
 % pytest

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,16 @@
 
 # Change Log
 
+## Jun-29-2024: Version 3.2.0
+
+- `--rd` and `--rd-fc2` options for generating random directional displacements.
+- Experimental implementation for using pypolymlp.
+
+## Jun-19-2024: Version 3.1.2
+
+- Treatment of numpy 2.0.
+- Experimental support of symfc.
+
 ## Jun-7-2024: Version 3.1.1
 
 - Minor fix related to typehint for python-3.8.