Merge pull request #31 from qchempku2017/atomate2_deprecation

[WIP] Atomate2 deprecation

.github/workflows/build.yml

@@ -1,46 +1,17 @@
-name: build-dist
+name: build
 
-# Use this workflow to manually trigger a build for testing purposes.
-# Download it from artifacts to test installation, or upload directly to PyPI.
-on:
-  workflow_dispatch:
-    inputs:
-      release-pypi:
-        required: true
-        type: boolean
-      CIBW_SKIP:
-        description: wheel builds to skip
+# Allowed to be referenced by another workflow.
+on: [workflow_dispatch, workflow_call]
 
 jobs:
 
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # No specific external lib to worry about.
-        os: [ubuntu-latest, windows-latest, macos-latest]
-    env:
-      CIBW_SKIP: pp*  ${{ github.event.inputs.CIBW_SKIP }}  # skip pypy wheels
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: wheelhouse/*.whl
-
+  # No need to build wheels.
   build_sdist:
     name: Build sdist
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Optional, use if you use setuptools_scm
 
@@ -50,21 +21,3 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
-
-  release-pypi:
-    needs: [build_wheels, build_sdist]
-    runs-on: ubuntu-latest
-    if: github.event.inputs.release-pypi == 'true'
-
-    steps:
-      - uses: actions/download-artifact@v3
-        with:
-          name: artifact
-          path: dist
-
-      - name: Publish package
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          verbose: true
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/docs.yml

@@ -1,6 +1,6 @@
 name: build-documentation
 
-on: workflow_dispatch
+on: [workflow_dispatch, workflow_call]
 
 jobs:
   docs:

.github/workflows/lint.yml

@@ -9,6 +9,10 @@ on:
     branches:
       - main
 
+  workflow_dispatch:
+
+  workflow_call:
+
 jobs:
   lint:
     runs-on: ubuntu-latest

.github/workflows/release.yml

@@ -1,125 +1,48 @@
 name: release
 
+# Releasing on push tags is less customizable compared to release upon request.
 on:
-  push:
-    tags:
-      - 'v[0-9]+.[0-9]+.[0-9]+'
+#  push:
+#    tags:
+#      - 'v[0-9]+.[0-9]+.[0-9]+'
+  release:
+    types: [published]
+    inputs:
+      release-pypi:
+        required: true
+        type: boolean
+        default: true
+  workflow_dispatch:
+    inputs:
+      release-pypi:
+        required: true
+        type: boolean
+        description: "if true a release is made on PyPI"
 
 jobs:
+  test:
+    uses: WFacer/WFacer/.github/workflows/test.yml@main
 
-  release-docs:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Install pandoc
-        run: sudo apt-get install pandoc
+  build:
+    needs: test
+    uses: WFacer/WFacer/.github/workflows/build.yml@main
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-optional.txt
-          pip install -e .[docs]
-
-      - name: Build docs
-        run: sphinx-build docs/src docs_build
-
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
-          publish_dir: ./docs_build
-
-  release-github:
-
-    runs-on: ubuntu-latest
-    needs:
-      - release-docs
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Get version
-        id: get_version
-        run: echo ::set-output name=VERSION::${GITHUB_REF#refs/tags/}
-
-      - name: Write release info  # CHANGES.md must be edited with the correct version being released.
-        run: awk 'BEGIN {p = 0} {a = 0 }; /\[v([0-9]|[1-9][0-9]*)\.([0-9]|[1-9][0-9]*)\.([0-9]|[1-9][0-9]*)(?:-([0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+([0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?\]/ { p += 1; a = 1}; p + a == 1 { print } ' CHANGES.md | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release.txt
-
-      - name: Release
-        uses: actions/create-release@v1
-        id: create_release
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ steps.get_version.outputs.VERSION }}
-          release_name: ${{ steps.get_version.outputs.VERSION }}
-          body_path: release.txt
-          draft: false
-          prerelease: false
-
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-
-    needs:
-      - release-github
-    strategy:
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-    env:
-      CIBW_SKIP: pp*  # skip pypy wheels
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: wheelhouse/*.whl
-
-  build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
-
-    needs:
-      - release-github
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0 # Optional, use if you use setuptools_scm
-
-      - name: Build sdist
-        run: pipx run build --sdist
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: dist/*.tar.gz
+  release-docs:
+    needs: test
+    uses: WFacer/WFacer/.github/workflows/docs.yml@main
 
   release-pypi:
+    needs: [build, docs]
     runs-on: ubuntu-latest
-    needs: [build_wheels, build_sdist]
+    if: github.event.inputs.release-pypi == 'true'
 
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
-      - name: Publish package
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           verbose: true
           user: __token__

.github/workflows/test.yml

@@ -1,5 +1,8 @@
 name: test
 
+env:
+  scip-version: 8.0.0
+
 on:
   push:
     branches:
@@ -9,9 +12,14 @@ on:
     branches:
       - main
 
+  workflow_call:
+
+  workflow_dispatch:
+
 jobs:
   test:
-    runs-on: ubuntu-latest
+    # Only 20.04 is known to work with scip 8.0.0
+    runs-on: ubuntu-20.04
     strategy:
       max-parallel: 10
       matrix:

.pre-commit-config.yaml

@@ -64,6 +64,7 @@ repos:
     additional_dependencies:
     - flake8-typing-imports==1.10.1
     - flake8-rst==0.8.0
+    - Flake8-pyproject
 
 - repo: https://github.com/pycqa/pydocstyle
   rev: 6.3.0  # pick a git hash / tag to point to

CHANGES.MD → CHANGES.md

@@ -4,5 +4,5 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v0.0.1](https://github.com/CederGroupHub/WFacer/tree/0.0.1) (2023-08-30)
+## [v0.0.0](https://github.com/CederGroupHub/WFacer/tree/0.0.0) (2023-08-30)
 Initial relatively *stable* version of the code.

WFacer/convergence.py

@@ -22,6 +22,7 @@ def compare_min_energy_structures_by_composition(min_e1, min_e2, matcher=None):
         matcher (StructureMatcher): optional
             A StructureMatcher used compare structures.
             wrangler.cluster_subspace._site_matcher is recommended.
+
     Return:
         float, bool:
             maximum energy difference in eV/site,
@@ -52,6 +53,7 @@ def compare_fitted_coefs(cluster_subspace, coefs_prev, coefs_now):
             Not ECIs because not divided by multiplicity!
         coefs_now(1d arrayLike):
             Cluster coefficients fitted in the latest iteration.
+
     Returns:
         float:
             || ECI' - ECI ||_1 / ||ECI||_1.
@@ -83,6 +85,7 @@ def ce_converged(
             must be equal to that of current iter_id - 1.
         convergence_options(dict):
             Pre-processed convergence criterion.
+
     Returns:
         bool.
     """

WFacer/enumeration.py

@@ -63,6 +63,7 @@ def enumerate_matrices(
             to 30, to prevent over-skewing.
         kwargs:
             keyword arguments to pass into SpaceGroupAnalyzer.
+
     Returns:
         List of 2D lists.
     """
@@ -222,6 +223,7 @@ def enumerate_compositions_as_counts(
 
     Results will be returned in "counts" format
     (see smol.moca.CompositionSpace).
+
     Args:
         sc_size(int):
             The super-cell size in the number of prim cells.
@@ -239,6 +241,7 @@ def enumerate_compositions_as_counts(
             Default to 1.
         kwargs:
             Other keyword arguments to initialize CompositionSpace.
+
     Returns:
         Enumerated possible compositions in "counts" format, not normalized:
             2D np.ndarray[int]
@@ -427,6 +430,7 @@ def generate_training_structures(
             before matching. It should be used with caution.
         kwargs:
             Keyword arguments for utils.selection.select_initial_rows.
+
     Returns:
         list[Structure], list[3*3 list[list[int]]], list[list[float]]:
             Initial training structures, super-cell matrices,

WFacer/fit.py

@@ -28,6 +28,7 @@ def fit_ecis_from_wrangler(
     """Fit ECIs from a fully processed wrangler.
 
     No weights will be used.
+
     Args:
         wrangler(CeDataWrangler):
             A CeDataWrangler storing all training structures.
@@ -60,6 +61,7 @@ def fit_ecis_from_wrangler(
             Other keyword arguments to initialize an optimizer.
         kwargs:
             Keyword arguments used by estimator._fit. For example, solver arguments.
+
     Returns:
         Estimator, 1D np.ndarray, float, float, float, 1D np.ndarray:
             Fitted estimator, coefficients (not ECIs), cross validation error (meV/site),