Merge branch 'main' into update/docker-container

.docker/cp2k-code.yml

@@ -2,7 +2,6 @@ label: cp2k
 computer: localhost
 description:
 input_plugin: cp2k
-on_computer: True
-remote_abs_path: /opt/conda/envs/cp2k/bin/cp2k.psmp
+filepath_executable: /opt/conda/envs/cp2k/bin/cp2k.psmp
 append_text:
 prepend_text: "conda activate cp2k"

.docker/init/add-codes.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+# Debugging
+set -x
+
+# Environment
+export SHELL=/bin/bash
+
+# Install cp2k code.
+verdi code show cp2k@localhost || verdi code create core.code.installed --config /home/aiida/aiida-cp2k/.docker/cp2k-code.yml --non-interactive

.docker/s6-rc.d/cp2k-code-setup/timeout-up

@@ -0,0 +1 @@
+0

.docker/s6-rc.d/cp2k-code-setup/type

@@ -0,0 +1 @@
+oneshot

.docker/s6-rc.d/cp2k-code-setup/up

@@ -0,0 +1,7 @@
+#!/command/execlineb -S0
+
+with-contenv
+
+foreground { s6-echo "Setting up CP2K code" }
+
+/etc/init/add-codes.sh

.flake8

@@ -1,10 +1,8 @@
 [flake8]
-# Recommend matching the black line length (default 88),
-# rather than using the flake8 default of 79:
 max-line-length = 88
 extend-ignore =
-    E501  # Line length handled by black.
-    W503  # Line break before binary operator, preferred formatting for black.
-    E203  # Whitespace before ':', preferred formatting for black.
+    E501
+    W503
+    E203
 exclude =
     docs/source/conf.py

.github/workflows/ci.yml

@@ -47,9 +47,9 @@ jobs:
     - name: Create container from aiida_cp2k_test image and test the plugin inside
       run: |
         export DOCKERID=`docker run -d aiida_cp2k_test`
-        docker exec --tty $DOCKERID wait-for-services
+        sleep 5
         docker logs $DOCKERID
-        docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
+        docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /home/aiida/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
 
 
   pre-commit:
@@ -68,7 +68,6 @@ jobs:
       run: |
         pip install --upgrade pip
         pip install -e .[dev,docs]
-        reentry scan
     - name: Run pre-commit
       run: |
         pre-commit install
@@ -90,7 +89,6 @@ jobs:
       run: |
         pip install --upgrade pip
         pip install -e .[docs,dev]
-        reentry scan
 
     - name: Build docs
       run: cd docs && make

.pre-commit-config.yaml

@@ -1,7 +1,10 @@
 ---
+ci:
+    autoupdate_schedule: quarterly
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
     hooks:
 
         - id: check-json
@@ -16,32 +19,32 @@ repos:
           exclude: *exclude_pre_commit_hooks
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.9.1
     hooks:
         - id: black
           language_version: python3 # Should be a command that runs python3.6+
           exclude: aiida_cp2k/workchains/base.py
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.1.0
     hooks:
         - id: flake8
           args: [--count, --show-source, --statistics]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
         - id: isort
           args: [--profile, black, --filter-files]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.32.1
+    rev: v3.14.0
     hooks:
         - id: pyupgrade
           args: [--py37-plus]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v1.5.1
     hooks:
         - id: mypy
           additional_dependencies:

Dockerfile

@@ -5,23 +5,23 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 
-FROM aiidateam/aiida-core:1.6.9
+
+FROM aiidateam/aiida-core-with-services:2.5.0
+
 
 # To prevent the container to exit prematurely.
 ENV KILL_ALL_RPOCESSES_TIMEOUT=50
 
-WORKDIR /opt/
-
-# Install CP2K from conda-forge.
 RUN conda create --yes -c conda-forge -n cp2k cp2k=9.1 && conda clean --all -f -y
 
 # Install aiida-cp2k plugin.
-COPY . aiida-cp2k
+COPY --chown="${SYSTEM_UID}:${SYSTEM_GID}" . /home/aiida/aiida-cp2k
 RUN pip install ./aiida-cp2k[dev,docs]
 
 # Install coverals.
 RUN pip install coveralls
 
 # Install the cp2k code.
-COPY .docker/opt/add-codes.sh /opt/
-COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/50_add-codes.sh
+COPY .docker/init/add-codes.sh /etc/init/
+COPY .docker/s6-rc.d/cp2k-code-setup /etc/s6-overlay/s6-rc.d/cp2k-code-setup
+COPY .docker/user/cp2k-code-setup /etc/s6-overlay/s6-rc.d/user/contents.d/cp2k-code-setup

README.md

@@ -1,9 +1,11 @@
-[![Build Status](https://travis-ci.org/aiidateam/aiida-cp2k.svg?branch=develop)](https://travis-ci.org/aiidateam/aiida-cp2k)
-[![Coverage Status](https://coveralls.io/repos/github/aiidateam/aiida-cp2k/badge.svg?branch=develop)](https://coveralls.io/github/aiidateam/aiida-cp2k?branch=develop)
 [![PyPI version](https://badge.fury.io/py/aiida-cp2k.svg)](https://badge.fury.io/py/aiida-cp2k)
-[![Documentation Status](https://readthedocs.org/projects/aiida-cp2k/badge/?version=latest)](https://aiida-cp2k.readthedocs.io/en/latest/?badge=latest)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-cp2k.svg)](https://pypi.python.org/pypi/aiida-cp2k/)
+[![Test CI](https://github.com/aiidateam/aiida-cp2k/actions/workflows/ci.yml/badge.svg)](https://github.com/aiidateam/aiida-cp2k/actions)
+[![Coverage Status](https://coveralls.io/repos/github/aiidateam/aiida-cp2k/badge.svg?branch=main)](https://coveralls.io/github/aiidateam/aiida-cp2k?branch=main)
+[![Documentation](https://readthedocs.org/projects/aiida-cp2k/badge/?version=latest)](https://aiida-cp2k.readthedocs.io/en/latest/?badge=latest)
 
 # AiiDA CP2K
+
 [AiiDA](http://www.aiida.net/) plugin for [CP2K](https://www.cp2k.org/).
 
 ## Installation
@@ -21,21 +23,66 @@ pip install -e .  # Also installs aiida, if missing (but not postgres/rabbitmq).
 ```
 
 ## Links
+
 * [Documentation](https://aiida-cp2k.readthedocs.io/en/latest/) for the calculation examples and features of the plugin.
 * [Make an issue](https://github.com/aiidateam/aiida-cp2k/issues/new) for bug reports, questions and suggestions.
 * [AiiDA](http://www.aiida.net/) to learn about AiiDA.
-* [Cp2k](https://www.cp2k.org/) to learn about CP2K.
+* [CP2K](https://www.cp2k.org/) to learn about CP2K.
+
+## For maintainers
+
+### Release
+
+To create a new release, clone the repository, install development dependencies with `pip install '.[dev]'`, and then execute `bumpver update --major/--minor/--patch`.
+This will:
+
+  1. Create a tagged release with bumped version and push it to the repository.
+  2. Trigger a GitHub actions workflow that creates a GitHub release.
+
+Additional notes:
+
+  - Use the `--dry` option to preview the release change.
+  - The release tag (e.g. a/b/rc) is determined from the last release.
+    Use the `--tag` option to override the release tag.
+
+### Testing
+
+To run the tests, you need to have Docker installed in your system.
+Once this is done, you can build the Docker image with the following command:
+
+```bash
+docker build -t aiida_cp2k_test .
+```
+Then, you can launch the container:
+
+```bash
+DOKERID=`docker run -it aiida_cp2k_test`
+```
+This will remeber the container ID in the variable `DOKERID`.
+You can then run the tests with the following command:
+
+```bash
+docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /home/aiida/aiida-cp2k/ && pytest'
+```
+
+To enter the container for manual testing do:
+
+```bash
+docker exec -it --user aiida $DOCKERID bash
+```
 
 
 ## License
-MIT
 
+MIT
 
 ## Contact
+
 [email protected]
 
 
 ## Acknowledgements
+
 This work is supported by:
 * the [MARVEL National Centre for Competency in Research](http://nccr-marvel.ch) funded by the [Swiss National Science Foundation](http://www.snf.ch/en);
 * the [MaX European Centre of Excellence](http://www.max-centre.eu/) funded by the Horizon 2020 EINFRA-5 program, Grant No. 676598;

aiida_cp2k/__init__.py

@@ -6,6 +6,6 @@
 ###############################################################################
 """The official AiiDA plugin for CP2K."""
 
-__version__ = "1.5.0"
+__version__ = "2.0.0"
 
 # EOF