CI updates

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/ci.yml

@@ -7,18 +7,24 @@ jobs:
   qa:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: pre-commit/action@v2.0.2
+      - uses: actions/checkout@v3
+      - uses: pre-commit/action@v3.0.0
 
   test:
     needs: qa
-    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8","3.9","3.10"]
+        os: [ubuntu-latest,macos-latest,windows-latest]
+
+    runs-on: ${{matrix.os}}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel

.github/workflows/combine-prs.yml

@@ -0,0 +1,151 @@
+name: 'Combine PRs'
+
+# Controls when the action will run - in this case triggered manually
+on:
+  workflow_dispatch:
+    inputs:
+      branchPrefix:
+        description: 'Branch prefix to find combinable PRs based on'
+        required: true
+        default: 'dependabot'
+      mustBeGreen:
+        description: 'Only combine PRs that are green (status is success)'
+        required: true
+        default: true
+      combineBranchName:
+        description: 'Name of the branch to combine PRs into'
+        required: true
+        default: 'combine-prs-branch'
+      ignoreLabel:
+        description: 'Exclude PRs with this label'
+        required: true
+        default: 'nocombine'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "combine-prs"
+  combine-prs:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - uses: actions/github-script@v6
+        id: create-combined-pr
+        name: Create Combined PR
+        with:
+          github-token: ${{secrets.GITHUB_TOKEN}}
+          script: |
+            const pulls = await github.paginate('GET /repos/:owner/:repo/pulls', {
+              owner: context.repo.owner,
+              repo: context.repo.repo
+            });
+            let branchesAndPRStrings = [];
+            let baseBranch = null;
+            let baseBranchSHA = null;
+            for (const pull of pulls) {
+              const branch = pull['head']['ref'];
+              console.log('Pull for branch: ' + branch);
+              if (branch.startsWith('${{ github.event.inputs.branchPrefix }}')) {
+                console.log('Branch matched prefix: ' + branch);
+                let statusOK = true;
+                if(${{ github.event.inputs.mustBeGreen }}) {
+                  console.log('Checking green status: ' + branch);
+                  const stateQuery = `query($owner: String!, $repo: String!, $pull_number: Int!) {
+                    repository(owner: $owner, name: $repo) {
+                      pullRequest(number:$pull_number) {
+                        commits(last: 1) {
+                          nodes {
+                            commit {
+                              statusCheckRollup {
+                                state
+                              }
+                            }
+                          }
+                        }
+                      }
+                    }
+                  }`
+                  const vars = {
+                    owner: context.repo.owner,
+                    repo: context.repo.repo,
+                    pull_number: pull['number']
+                  };
+                  const result = await github.graphql(stateQuery, vars);
+                  const [{ commit }] = result.repository.pullRequest.commits.nodes;
+                  const state = commit.statusCheckRollup.state
+                  console.log('Validating status: ' + state);
+                  if(state != 'SUCCESS') {
+                    console.log('Discarding ' + branch + ' with status ' + state);
+                    statusOK = false;
+                  }
+                }
+                console.log('Checking labels: ' + branch);
+                const labels = pull['labels'];
+                for(const label of labels) {
+                  const labelName = label['name'];
+                  console.log('Checking label: ' + labelName);
+                  if(labelName == '${{ github.event.inputs.ignoreLabel }}') {
+                    console.log('Discarding ' + branch + ' with label ' + labelName);
+                    statusOK = false;
+                  }
+                }
+                if (statusOK) {
+                  console.log('Adding branch to array: ' + branch);
+                  const prString = '#' + pull['number'] + ' ' + pull['title'];
+                  branchesAndPRStrings.push({ branch, prString });
+                  baseBranch = pull['base']['ref'];
+                  baseBranchSHA = pull['base']['sha'];
+                }
+              }
+            }
+            if (branchesAndPRStrings.length == 0) {
+              core.setFailed('No PRs/branches matched criteria');
+              return;
+            }
+            try {
+              await github.rest.git.createRef({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                ref: 'refs/heads/' + '${{ github.event.inputs.combineBranchName }}',
+                sha: baseBranchSHA
+              });
+            } catch (error) {
+              console.log(error);
+              core.setFailed('Failed to create combined branch - maybe a branch by that name already exists?');
+              return;
+            }
+
+            let combinedPRs = [];
+            let mergeFailedPRs = [];
+            for(const { branch, prString } of branchesAndPRStrings) {
+              try {
+                await github.rest.repos.merge({
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  base: '${{ github.event.inputs.combineBranchName }}',
+                  head: branch,
+                });
+                console.log('Merged branch ' + branch);
+                combinedPRs.push(prString);
+              } catch (error) {
+                console.log('Failed to merge branch ' + branch);
+                mergeFailedPRs.push(prString);
+              }
+            }
+
+            console.log('Creating combined PR');
+            const combinedPRsString = combinedPRs.join('\n');
+            let body = '✅ This PR was created by the Combine PRs action by combining the following PRs:\n' + combinedPRsString;
+            if(mergeFailedPRs.length > 0) {
+              const mergeFailedPRsString = mergeFailedPRs.join('\n');
+              body += '\n\n⚠️ The following PRs were left out due to merge conflicts:\n' + mergeFailedPRsString
+            }
+            await github.rest.pulls.create({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              title: 'Combined PR',
+              head: '${{ github.event.inputs.combineBranchName }}',
+              base: baseBranch,
+              body: body
+            });

.readthedocs.yaml

@@ -0,0 +1,10 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py

README.md

@@ -75,7 +75,7 @@ List of modules
 Requirements
 ------------
 
-The main language is Python 3 and has been tested using Python 3.6+.
+The main language is Python 3 and has been tested using Python 3.8+.
 Basic requirements are Numpy and Scipy.
 The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE),  [spglib](http://atztogo.github.io/spglib), and [pymatgen](www.pymatgen.org) are also required for many components.
 

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+# Minimum requirements for the build system to execute.
+requires = ["setuptools"]  # PEP 508 specifications.
+
+[tool.semantic_release]
+version_variable = "setup.py:__version__"
+version_source = "tag"

requirements-dev.txt

@@ -1,6 +1,6 @@
-pre-commit
-black
-isort
-pytest
-nbqa
-pyupgrade
+pre-commit ==2.20.0
+black ==22.12.0
+isort ==5.11.2
+pytest ==7.2.0
+nbqa ==1.5.3
+pyupgrade ==3.3.1

requirements.txt

@@ -1,10 +1,10 @@
-numpy >= 1.14.3
-scipy
-spglib
-future
-ase
-pymatgen >=2022.0.0
-pandas >= 0.24
-pathos
-pytest
-pytest-subtests
+numpy == 1.23.3
+scipy ==1.9.1
+spglib ==1.16.5
+future ==0.18.2
+ase ==3.22.1
+pymatgen ==2022.9.21
+pandas == 1.5.0
+pathos ==0.2.9
+pytest ==7.2.0
+pytest-subtests ==0.9.0

setup.py

@@ -17,7 +17,7 @@
 if __name__ == "__main__":
     setup(
         name="SMACT",
-        version="2.4.2",
+        version=__version__,
         description="Semiconducting Materials by Analogy and Chemical Theory",
         long_description=open(os.path.join(module_dir, "README.md")).read(),
         long_description_content_type="text/markdown",