Release/22.06.0a1 (#260)

aiidalab · Jun 22, 2022 · 39aeb65 · 39aeb65
2 parents 50e6ec9 + 8feadfb
commit 39aeb65
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diff --git a/.github/workflows/build_and_test_on_pr.yml b/.github/workflows/build_and_test_on_pr.yml
@@ -1,5 +1,6 @@
+---
 # Test the Docker image on every pull request.
-# 
+#
 # The steps are:
 # 1. Build docker image using cached data.
 # 2. Start the docker container with local folder mounted to it.
@@ -9,66 +10,57 @@
 
 name: build-and-test-image-from-pull-request
 
-on:
-  [pull_request]
+on: [pull_request]
 
 jobs:
 
-  build-and-test:
+    build-and-test:
 
-    runs-on: ubuntu-latest
-    timeout-minutes: 45
+        runs-on: ubuntu-latest
+        timeout-minutes: 45
 
-    steps:
-      -
-        uses: actions/checkout@v2
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
-      -
-        name: Cache Docker layers
-        uses: actions/cache@v2
-        with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ github.sha }}
-          restore-keys: |
-            ${{ runner.os }}-buildx-
-      -
-        name: Build image locally
-        uses: docker/build-push-action@v2
-        with:
-          load: true
-          push: false
-          tags: aiidalab-docker-stack:latest
-          cache-from: type=local,src=/tmp/.buildx-cache
-          cache-to: type=local,dest=/tmp/.buildx-cache
-      -
-        name: Start and test the container
-        id: test_run
-        run: |
-          mkdir tmp
-          export DOCKERID=`docker run -v $PWD/tmp:/home/aiida -d aiidalab-docker-stack:latest`
-          echo "::set-output name=docker_id_first_run::${DOCKERID}"
-          docker exec --tty --user root $DOCKERID wait-for-services
-          docker exec --tty --user aiida $DOCKERID wait-for-services
-          docker exec --tty --user aiida $DOCKERID /bin/bash -l -c '/usr/lib/postgresql/10/bin/pg_ctl -D /home/$SYSTEM_USER/.postgresql status' # Check that postgres is up.
-          docker exec --tty --user root $DOCKERID /bin/bash -l -c 'service rabbitmq-server status' # Check that rabbitmq is up.
-          docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'conda create -y -n test_env python=3.8' # Check that one can create a new conda environment.
-          docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'conda activate test_env' # Check that new environment works.
-          sudo cp tmp/.ssh/id_rsa . # Copy id_rsa file from the mounted folder.
-          docker stop $DOCKERID # Stop the container.
-          export DOCKERID=`docker run -v $PWD/tmp:/home/aiida -d aiidalab-docker-stack:latest` # Start a new container using the same mounted folder.
-          echo "::set-output name=docker_id_second_run::${DOCKERID}"
-          docker exec --tty $DOCKERID wait-for-services
-          sudo diff id_rsa tmp/.ssh/id_rsa # Check that the id_rsa file wasn't modified.
-      -
-        name: Show the container log (first run).
-        if: always()
-        run: docker logs "${{ steps.test_run.outputs.docker_id_first_run }}"
-      -
-        name: Show the container log (second run).
-        if: always()
-        run: docker logs "${{ steps.test_run.outputs.docker_id_second_run }}"
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up QEMU
+              uses: docker/setup-qemu-action@v1
+            - name: Set up Docker Buildx
+              uses: docker/setup-buildx-action@v1
+            - name: Cache Docker layers
+              uses: actions/cache@v2
+              with:
+                  path: /tmp/.buildx-cache
+                  key: ${{ runner.os }}-buildx-${{ github.sha }}
+                  restore-keys: |
+                      ${{ runner.os }}-buildx-
+            - name: Build image locally
+              uses: docker/build-push-action@v2
+              with:
+                  load: true
+                  push: false
+                  tags: aiidalab-docker-stack:latest
+                  cache-from: type=local,src=/tmp/.buildx-cache
+                  cache-to: type=local,dest=/tmp/.buildx-cache
+            - name: Start and test the container
+              id: test_run
+              run: |
+                  mkdir tmp
+                  export DOCKERID=`docker run -v $PWD/tmp:/home/aiida -d aiidalab-docker-stack:latest`
+                  echo "::set-output name=docker_id_first_run::${DOCKERID}"
+                  docker exec --tty --user root $DOCKERID wait-for-services
+                  docker exec --tty --user aiida $DOCKERID wait-for-services
+                  docker exec --tty --user aiida $DOCKERID /bin/bash -l -c '/usr/lib/postgresql/12/bin/pg_ctl -D /home/$SYSTEM_USER/.postgresql status' # Check that postgres is up.
+                  docker exec --tty --user root $DOCKERID /bin/bash -l -c 'service rabbitmq-server status' # Check that rabbitmq is up.
+                  docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'conda create -y -n test_env python=3.8' # Check that one can create a new conda environment.
+                  docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'conda activate test_env' # Check that new environment works.
+                  sudo cp tmp/.ssh/id_rsa . # Copy id_rsa file from the mounted folder.
+                  docker stop $DOCKERID # Stop the container.
+                  export DOCKERID=`docker run -v $PWD/tmp:/home/aiida -d aiidalab-docker-stack:latest` # Start a new container using the same mounted folder.
+                  echo "::set-output name=docker_id_second_run::${DOCKERID}"
+                  docker exec --tty $DOCKERID wait-for-services
+                  sudo diff id_rsa tmp/.ssh/id_rsa # Check that the id_rsa file wasn't modified.
+            - name: Show the container log (first run).
+              if: always()
+              run: docker logs "${{ steps.test_run.outputs.docker_id_first_run }}"
+            - name: Show the container log (second run).
+              if: always()
+              run: docker logs "${{ steps.test_run.outputs.docker_id_second_run }}"
diff --git a/.github/workflows/release_image.yml b/.github/workflows/release_image.yml
@@ -1,50 +1,45 @@
+---
 # Build and push image to DockerHub
 
 name: release-image
 
 on:
-  push:
-    branches:
-      - master
-      - develop
-    tags:
-      - "v[0-9]+.[0-9]+.[0-9]+*"
+    push:
+        branches:
+            - master
+            - develop
+        tags:
+            - v[0-9]+.[0-9]+.[0-9]+*
 
 jobs:
 
-  build-docker-image:
+    build-docker-image:
 
-    runs-on: ubuntu-latest
-    timeout-minutes: 45
+        runs-on: ubuntu-latest
+        timeout-minutes: 45
 
-    steps:
-      -
-        uses: actions/checkout@v2
-      -
-        name: Docker meta
-        id: meta
-        uses: docker/metadata-action@v3
-        with:
-          images: ${{ github.repository }}
-          tags: |
-            type=ref,event=branch
-            type=match,pattern=v(.*),group=1
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
-      -
-        name: Login to DockerHub
-        uses: docker/login-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      -
-        name: Build and push
-        id: docker_build
-        uses: docker/build-push-action@v2
-        with:
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
+        steps:
+            - uses: actions/checkout@v2
+            - name: Docker meta
+              id: meta
+              uses: docker/metadata-action@v3
+              with:
+                  images: ${{ github.repository }}
+                  tags: |
+                      type=ref,event=branch
+                      type=match,pattern=v(.*),group=1
+            - name: Set up QEMU
+              uses: docker/setup-qemu-action@v1
+            - name: Set up Docker Buildx
+              uses: docker/setup-buildx-action@v1
+            - name: Login to DockerHub
+              uses: docker/login-action@v1
+              with:
+                  username: ${{ secrets.DOCKER_USERNAME }}
+                  password: ${{ secrets.DOCKER_PASSWORD }}
+            - name: Build and push
+              id: docker_build
+              uses: docker/build-push-action@v2
+              with:
+                  push: true
+                  tags: ${{ steps.meta.outputs.tags }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,20 @@
+---
+repos:
+
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.3.0
+      hooks:
+          - id: check-json
+          - id: check-yaml
+          - id: end-of-file-fixer
+          - id: trailing-whitespace
+
+    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+      rev: 0.2.1
+      hooks:
+          - id: yamlfmt
+
+    - repo: https://github.com/sirosen/check-jsonschema
+      rev: 0.16.0
+      hooks:
+          - id: check-github-workflows
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM aiidateam/aiida-core:1.6.5-bionic
+FROM aiidateam/aiida-core:1.6.8
 
 LABEL maintainer="AiiDAlab Team <[email protected]>"
 
@@ -58,7 +58,7 @@ RUN /usr/bin/pip3 install --upgrade pip
 # Jupyter dependencies installed into system python environment
 # which runs the jupyter notebook server.
 COPY requirements-server.txt .
-RUN /usr/local/bin/pip install -r /opt/requirements-server.txt \ 
+RUN /usr/local/bin/pip install -r /opt/requirements-server.txt \
     && /usr/local/bin/pip cache purge
 
 # Install and enable appmode.
@@ -75,7 +75,7 @@ RUN /usr/local/bin/jupyter serverextension enable --py --sys-prefix appmode
 #     npm install && \
 #     npm run build && \
 #     npm run build:webpack && \
-#     npm pack ./ && \ 
+#     npm pack ./ && \
 #     /usr/local/bin/jupyter labextension install *.tgz && \
 #    cd ..
 

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -20,7 +20,7 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 
---- 
+---
 
 The 'fix-permissions' script is licensed under the terms of the Modified BSD License
 (also known as New or Revised or 3-Clause BSD), as follows:

diff --git a/opt/start-notebook.sh b/opt/start-notebook.sh
@@ -32,5 +32,3 @@ else
       --VoilaConfiguration.enable_nbextensions=True                  \
       --NotebookApp.default_url="/apps/apps/home/start.ipynb"
 fi
-
-
diff --git a/requirements-server.txt b/requirements-server.txt
@@ -1,7 +1,7 @@
 # Dependencies for notebook server and interaction with JupyterHub
 jupyterhub==1.5.0
 jupyterlab==3.0.17
-notebook==6.4.1
+notebook==6.4.12
 # Detect notebooks written in MyST Markdown
 jupytext==1.13.4
 # Dependencies for jupyter widgets
@@ -11,7 +11,7 @@ ipywidgets-extended==1.0.5
 nglview==2.7.7
 widget-periodictable==2.1.5
 # Used for exposing AiiDA REST API to the outside world
-jupyter-server-proxy==3.1.0
+jupyter-server-proxy==3.2.1
 # Install voila package and AiiDAlab voila template.
 voila==0.2.10
 voila-aiidalab-template==0.2.1
diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
-aiidalab==21.11.1
-aiidalab-widgets-base==1.1.1
+aiidalab==22.02.0
+aiidalab-widgets-base==1.3.3
 binaryornot~=0.4
 bokeh~=2.0
 bqplot~=0.12
Original file line number	Diff line number	Diff line change
Expand Up		@@ -32,5 +32,3 @@ else
		--VoilaConfiguration.enable_nbextensions=True \
		--NotebookApp.default_url="/apps/apps/home/start.ipynb"
		fi