Add new symmetry fields to structure model

.github/fly.toml

@@ -1,11 +1,17 @@
-# fly.toml file generated for broken-field-1976 on 2022-11-21T21:37:55Z
-
 app = "optimade"
 kill_signal = "SIGINT"
 kill_timeout = 5
+swap_size_mb = 1024
 processes = []
 
+[build]
+  builder = "paketobuildpacks/builder:base"
+
 [env]
+PORT = 5000
+BPE_OPTIMADE_CONFIG_FILE = "./tests/test_config.json"
+BPL_OPTIMADE_CONFIG_FILE = "./tests/test_config.json"
+OPTIMADE_CONFIG_FILE = "./tests/test_config.json"
 
 [experimental]
   allowed_public_ports = []
@@ -36,9 +42,3 @@ processes = []
     interval = "15s"
     restart_limit = 0
     timeout = "2s"
-
-[build]
-  builtin = "python"
-
-[build.settings]
-  pythonbase = "3.10-slim-buster"

.github/workflows/cd_release.yml

@@ -6,26 +6,44 @@ on:
     - published
 
 env:
-  PUBLISH_UPDATE_BRANCH: master
   GIT_USER_NAME: OPTIMADE Developers
   GIT_USER_EMAIL: "dev@optimade.org"
+  DEFAULT_RELEASE_BRANCH: "master"
 
 jobs:
 
   publish:
     name: Publish OPTIMADE Python tools
     runs-on: ubuntu-latest
     if: github.repository == 'Materials-Consortia/optimade-python-tools' && startsWith(github.ref, 'refs/tags/v')
+    outputs:
+      publish_branch: ${{ steps.save_branch.outputs.publish_branch }}
 
     steps:
-    - name: Checkout repository
+    - name: Get triggering branch
+      uses: octokit/request-action@v2.x
+      id: get_release_branch
+      with:
+        route: GET /repos/{owner}/{repo}/releases/tags/${{ github.ref_name }}
+        owner: Materials-Consortia
+        repo: optimade-python-tools
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Save branch name
+      id: save_branch
+      run: |
+        echo 'publish_branch=${{ fromJson(steps.get_release_branch.outputs.data).target_commitish }}' >> $GITHUB_OUTPUT
+
+    - name: Checkout publish branch
       uses: actions/checkout@v4
       with:
         submodules: true
         fetch-depth: 0
+        branch: ${{ steps.save_branch.outputs.publish_branch }}
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
 
@@ -36,21 +54,26 @@ jobs:
         pip install -r requirements.txt -r requirements-dev.txt -r requirements-client.txt -r requirements-http-client.txt -r requirements-docs.txt
         pip install -e .[all]
 
+    - name: Get base branch name for tag
+      id: branch_finder
+      run:
+        echo "branch=$(git branch --show-current)" >> "$GITHUB_OUTPUT"
+
     - name: Update changelog
       uses: CharMixer/auto-changelog-action@v1
       with:
         token: ${{ secrets.RELEASE_PAT_BOT }}
-        release_branch: ${{ env.PUBLISH_UPDATE_BRANCH }}
+        release_branch: ${{ steps.save_branch.outputs.publish_branch }}
         exclude_labels: "duplicate,question,invalid,wontfix,dependency_updates,skip_changelog"
 
     - name: Update API Reference docs and version - Commit changes and update tag
       run: .github/utils/update_docs.sh
 
-    - name: Update '${{ env.PUBLISH_UPDATE_BRANCH }}'
+    - name: Update triggering branch
       uses: CasperWA/push-protected@v2
       with:
         token: ${{ secrets.RELEASE_PAT_BOT }}
-        branch: ${{ env.PUBLISH_UPDATE_BRANCH }}
+        branch: ${{ steps.save_branch.outputs.publish_branch }}
         unprotect_reviews: true
         sleep: 15
         force: true
@@ -63,7 +86,7 @@ jobs:
       uses: CharMixer/auto-changelog-action@v1
       with:
         token: ${{ secrets.RELEASE_PAT_BOT }}
-        release_branch: ${{ env.PUBLISH_UPDATE_BRANCH }}
+        release_branch: ${{ steps.save_branch.outputs.publish_branch }}
         since_tag: "${{ env.PREVIOUS_VERSION }}"
         output: "release_changelog.md"
         exclude_labels: "duplicate,question,invalid,wontfix,dependency_updates,skip_changelog"
@@ -96,10 +119,10 @@ jobs:
       with:
         submodules: true
         fetch-depth: 0
-        ref: ${{ env.PUBLISH_UPDATE_BRANCH }}
+        ref: ${{ needs.publish.outputs.publish_branch }}
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
 
@@ -115,18 +138,23 @@ jobs:
         git config --global user.name "${{ env.GIT_USER_NAME }}"
         git config --global user.email "${{ env.GIT_USER_EMAIL }}"
 
-    - name: Deploy documentation
+    - name: Deploy versioned documentation
+      run: |
+        mike deploy --push --remote origin --branch gh-pages --config-file mkdocs.yml ${GITHUB_REF#refs/tags/v}
+
+    - name: Deploy stable/latest documentation
+      if: ${{ needs.publish.outputs.publish_branch }} == ${{ env.DEFAULT_RELEASE_BRANCH }}
       run: |
         mike deploy --push --remote origin --branch gh-pages --update-aliases --config-file mkdocs.yml ${GITHUB_REF#refs/tags/v} stable
-        mike deploy --push --remote origin --branch gh-pages --update-aliases --config-file mkdocs.yml latest master
+        mike deploy --push --remote origin --branch gh-pages --update-aliases --config-file mkdocs.yml latest ${{ env.DEFAULT_RELEASE_BRANCH }}
 
   publish_container_image:
     name: Publish container image
     needs: publish
     uses: ./.github/workflows/cd_container_image.yml
     with:
       release: true
-      checkout_ref: master
+      checkout_ref: ${{ needs.publish.outputs.publish_branch }}
     secrets: inherit
     permissions:
       packages: write

.github/workflows/ci.yml

@@ -9,6 +9,7 @@ on:
 
 env:
   PYTEST_ADDOPTS: "--color=yes"
+  LINTING_PY_VERSION: "3.9"  # The version of Python to use for linting (typically the minimum supported)
 
 # Cancel running workflows when additional changes are pushed
 # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
@@ -26,10 +27,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python ${{ env.LINTING_PY_VERSION }}
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: ${{ env.LINTING_PY_VERSION }}
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -56,10 +57,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python ${{ env.LINTING_PY_VERSION }}
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: ${{ env.LINTING_PY_VERSION }}
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -131,7 +132,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     services:
       mongo:
@@ -167,7 +168,7 @@ jobs:
         fetch-depth: 2
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -184,25 +185,25 @@ jobs:
         pip install -r requirements-http-client.txt
 
     - name: Run non-server tests
-      run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml tests/ --ignore tests/server
+      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml tests/ --ignore tests/server
 
     - name: Install latest server dependencies
       run: pip install -r requirements-server.txt
 
     - name: Run server tests (using `mongomock`)
-      run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
 
     - name: Run server tests with no API validation (using `mongomock`)
       run:
-        pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+        pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
         OPTIMADE_VALIDATE_API_RESPONSE: false
 
     - name: Run server tests (using a real MongoDB)
-      run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongodb'
 
@@ -227,36 +228,38 @@ jobs:
       run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/adapters/
 
     - name: Run tests for validator only to assess coverage (mongomock)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == '3.11'
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
 
     - name: Run tests for validator only to assess coverage (Elasticsearch)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == '3.11'
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'elastic'
         OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data
 
     - name: Run tests for validator only to assess coverage (MongoDB)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == '3.11'
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongodb'
         OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data
 
     - name: Run the OPTIMADE Client CLI
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == '3.11'
       run: |
         coverage run --append --source optimade optimade/client/cli.py \
            --filter 'nsites = 1' \
+           --http-timeout 1.0 \
            --output-file test_get_async.json \
            https://optimade.fly.dev
         test test_get_async.json
 
         coverage run --append --source optimade optimade/client/cli.py \
           --filter 'nsites = 1' \
+           --http-timeout 1.0 \
           --count \
           --output-file test_count.json \
           https://optimade.fly.dev
@@ -265,6 +268,7 @@ jobs:
         coverage run --append --source optimade optimade/client/cli.py \
           --no-async \
           --filter 'nsites = 1' \
+           --http-timeout 1.0 \
           --count \
           --output-file test_count_no_async.json \
           https://optimade.fly.dev
@@ -275,17 +279,19 @@ jobs:
         coverage xml
 
     - name: Upload coverage to Codecov
-      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
-      uses: codecov/codecov-action@v3
+      if: matrix.python-version == '3.11' && github.repository == 'Materials-Consortia/optimade-python-tools'
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         name: project
         file: ./coverage.xml
         flags: project
 
     - name: Upload validator coverage to Codecov
-      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
-      uses: codecov/codecov-action@v3
+      if: matrix.python-version == '3.11' && github.repository == 'Materials-Consortia/optimade-python-tools'
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         name: validator
         file: ./validator_cov.xml
         flags: validator
@@ -298,9 +304,9 @@ jobs:
       with:
         submodules: true
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: ${{ env.LINTING_PY_VERSION }}
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -330,10 +336,10 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python ${{ env.LINTING_PY_VERSION }}
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: ${{ env.LINTING_PY_VERSION }}
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt

.github/workflows/ci_cd_updated_master.yml

@@ -43,11 +43,11 @@ jobs:
         fetch-depth: 0
         submodules: true
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.9
       if: env.RELEASE_RUN == 'false'
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.9'
 
     - name: Install dependencies
       if: env.RELEASE_RUN == 'false'
@@ -138,8 +138,6 @@ jobs:
   deploy-fly:
     env:
         FLY_API_TOKEN: ${{ secrets.FLY_API_TOKEN }}
-        OPTIMADE_CONFIG_FILE: /app/tests/test_config.json
-        OPTIMADE_BASE_URL: https://optimade.fly.dev
     runs-on: ubuntu-latest
     if: github.repository_owner == 'Materials-Consortia'
     steps:
@@ -152,6 +150,10 @@ jobs:
     - name: Set up Fly
       uses: superfly/flyctl-actions/setup-flyctl@master
 
+    - name: Combine requirements for builder
+      run: |
+        cat requirements-server.txt >> requirements.txt
+
     - name: Deploy to Fly
       run: flyctl deploy --remote-only -c ./.github/fly.toml