Merge pull request #3934 from aiidateam/release/1.2.0

Release `v1.2.0`

.ci/workchains.py

@@ -7,6 +7,7 @@
 # For further information on the license, see the LICENSE.txt file        #
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
+# pylint: disable=invalid-name
 from aiida.common import AttributeDict
 from aiida.engine import calcfunction, workfunction, WorkChain, ToContext, append_, while_, ExitCode
 from aiida.engine import BaseRestartWorkChain, process_handler, ProcessHandlerReport

.coveragerc

@@ -1,6 +1,5 @@
 [run]
 source = aiida
-omit = aiida/test*.py,aiida/*/test*.py,aiida/*/*/test*.py,aiida/*/*/*/test*.py,aiida/*/*/*/*/test*.py,aiida/*/*/*/*/*/test*.py,aiida/*/migrations/*.py,aiida/*/migrations/versions/*.py
 
 [html]
 directory = .ci/coverage/html

.github/CODEOWNERS

@@ -0,0 +1,10 @@
+# All files related to dependency management are owned by the
+# currently active dependency manager (DM) to trigger an automatic review
+# request from the DM upon changes. Please see AEP-002 for details:
+# https://github.com/aiidateam/AEP/tree/master/002_dependency_management
+setup.*                         @aiidateam/dependency-manager
+environment.yml                 @aiidateam/dependency-manager
+requirements*.txt               @aiidateam/dependency-manager
+pyproject.toml                  @aiidateam/dependency-manager
+utils/dependency_management.py  @aiidateam/dependency-manager
+.github/workflows/dm.yml        @aiidateam/dependency-manager

.github/config/profile.yaml

@@ -11,4 +11,4 @@ db_port: 5432
 db_name: PLACEHOLDER_DATABASE_NAME
 db_username: postgres
 db_password: ''
-repository: PLACEHOLDER_REPOSITORY
+repository: PLACEHOLDER_REPOSITORY

.github/workflows/ci.yml

@@ -1,35 +1,16 @@
-name: aiida-core
+name: continuous-integration
 
 on: [push, pull_request]
 
 jobs:
 
-  conda:
-
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-
-    steps:
-    - uses: actions/checkout@v1
-
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-
-    - name: Conda install
-      env:
-        PYTHON_VERSION: 3.7
-      run:
-        .github/workflows/conda.sh
-
   docs:
 
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v1
@@ -60,7 +41,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v1
@@ -83,6 +64,41 @@ jobs:
       run:
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
+  check-requirements:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dm-script dependencies
+      run: pip install packaging==20.3 click~=7.0 pyyaml~=5.1 toml
+
+    - name: Check requirements files
+      run: python ./utils/dependency_management.py check-requirements DEFAULT
+
+    - name: Create commit comment
+      if: failure()
+      uses: peter-evans/commit-comment@v1
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        path: setup.json
+        body: |
+          It appears that at least one of the environments defined in the requirements files
+          ('requirements/*.txt') is not meeting the dependencies specified in the 'setup.json' file.
+          These files define the environment for continuous integration tests, so it is important that they are updated.
+
+          If this commit is part of a pull request, you can automatically update the requirements by
+          commenting with '/update-requirements'.
+
+          Click [here](https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management) for more information.
+
   tests:
 
     runs-on: ubuntu-latest
@@ -91,18 +107,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.5, 3.8]
         backend: ['django', 'sqlalchemy']
+        python-version: [3.5, 3.8]
+
+    services:
+      postgres:
+        image: postgres:10
+        env:
+          POSTGRES_DB: test_${{ matrix.backend }}
+          POSTGRES_PASSWORD: ''
+          POSTGRES_HOST_AUTH_METHOD: trust
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+      rabbitmq:
+        image: rabbitmq:latest
+        ports:
+          - 5672:5672
 
     steps:
-    - uses: actions/checkout@v1
-    - uses: CasperWA/[email protected]
-      with:
-        postgresql version: '10'
-        postgresql db: test_${{ matrix.backend }}
-        postgresql user: postgres
-        postgresql password: ''
-        postgresql auth: trust
+    - uses: actions/checkout@v2
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
@@ -111,20 +139,25 @@ jobs:
 
     - name: Install system dependencies
       run: |
-        wget -O - "https://github.com/rabbitmq/signing-keys/releases/download/2.0/rabbitmq-release-signing-key.asc" | sudo apt-key add -
-        echo 'deb https://dl.bintray.com/rabbitmq-erlang/debian bionic erlang' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
-        echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
         sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
         sudo apt update
-        sudo apt install postgresql-10 rabbitmq-server graphviz
-        sudo systemctl status rabbitmq-server.service
+        sudo apt install postgresql-10 graphviz
 
-    - name: Install python dependencies
+    - name: Upgrade pip
       run: |
         pip install --upgrade pip
-        pip install numpy==1.17.4
-        pip install -e .[atomic_tools,docs,notebook,rest,testing]
+        pip --version
+
+    - name: upgrade setuptools [py35]
+      if: matrix.python-version == 3.5
+      run: pip install -I setuptools==38.2.0  # Minimally required version for Python 3.5.
+
+    - name: Install aiida-core
+      run: |
+        pip install -r requirements/requirements-py-${{ matrix.python-version }}.txt
+        pip install --no-deps -e .
         reentry scan
+        pip freeze
 
     - name: Setup environment
       env:
@@ -138,13 +171,22 @@ jobs:
       run:
         .github/workflows/tests.sh
 
+    - name: Upload coverage report
+      if: matrix.python-version == 3.5 && github.repository == 'aiidateam/aiida-core'
+      uses: codecov/codecov-action@v1
+      with:
+        name: aiida-pytests-py3.5-${{ matrix.backend }}
+        flags: ${{ matrix.backend }}
+        file: ./coverage.xml
+        fail_ci_if_error: true
+
   verdi:
 
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
 
     - name: Set up Python 3.7
       uses: actions/setup-python@v1
@@ -166,7 +208,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
 
     - name: Install docker
       run: |

.github/workflows/test-install.yml

@@ -0,0 +1,157 @@
+name: test-install
+
+on:
+  pull_request:
+    paths:
+      - 'setup.*'
+      - 'environment.yml'
+      - '**/requirements*.txt'
+      - 'pyproject.toml'
+      - 'util/dependency_management.py'
+      - '.github/workflows/test-install.yml'
+  schedule:
+    - cron: '30 02 * * *'  # nightly build
+
+jobs:
+
+  validate-dependency-specification:
+    # Note: The specification is also validated by the pre-commit hook.
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Install dm-script dependencies
+      run: pip install packaging==20.3 click~=7.0 pyyaml~=5.1 toml
+
+    - name: Validate
+      run: python ./utils/dependency_management.py validate-all
+
+  install-with-pip:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Pip install
+      run: |
+        python -m pip install -e .
+        python -m pip freeze
+
+    - name: Test importing aiida
+      run:
+        python -c "import aiida"
+
+  install-with-conda:
+
+    runs-on: ubuntu-latest
+    name: install-with-conda
+
+    timeout-minutes: 5
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setup Conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: 3.7
+    - run: conda --version
+    - run: python --version
+    - run: which python
+
+    - name: Create conda environment
+      run: |
+        conda env create -f environment.yml -n test-environment
+        source activate test-environment
+        python -m pip install --no-deps -e .
+
+    - name: Test importing aiida
+      run: |
+        source activate test-environment
+        python -c "import aiida"
+
+  tests:
+
+    needs: [install-with-pip, install-with-conda]
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.5, 3.6, 3.7, 3.8]
+        backend: ['django', 'sqlalchemy']
+
+    services:
+      postgres:
+        image: postgres:10
+        env:
+          POSTGRES_DB: test_${{ matrix.backend }}
+          POSTGRES_PASSWORD: ''
+          POSTGRES_HOST_AUTH_METHOD: trust
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+      rabbitmq:
+        image: rabbitmq:latest
+        ports:
+          - 5672:5672
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
+        sudo apt update
+        sudo apt install postgresql-10 graphviz
+
+    - run: pip install --upgrade pip
+
+    - name: upgrade setuptools [py35]
+      if: matrix.python-version == 3.5
+      run: pip install -I setuptools==38.2.0
+
+    - name: Install aiida-core
+      run: |
+        pip install -e .[atomic_tools,docs,notebook,rest,testing]
+        reentry scan
+
+    - run: pip freeze
+
+    - name: Setup AiiDA environment
+      env:
+        AIIDA_TEST_BACKEND: ${{ matrix.backend }}
+      run:
+        .github/workflows/setup.sh
+
+    - name: Run test suite
+      env:
+        AIIDA_TEST_BACKEND: ${{ matrix.backend }}
+      run:
+        .github/workflows/tests.sh