Merge pull request #57 from yakutovicha/release_1.0.0

Release 1.0.0
lsmo-epfl · Feb 13, 2020 · f4327ce · f4327ce
2 parents 5748113 + 149bb2d
commit f4327ce
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diff --git a/.docker/my_init.d/add-codes.sh b/.docker/my_init.d/add-codes.sh
@@ -1,4 +1,7 @@
 #!/bin/bash
 set -em
 
-su -c /opt/add-codes.sh aiida
+su -c /opt/add-codes.sh ${SYSTEM_USER}
+
+# Make /opt/aiida-raspa folder editable for the $SYSTEM_USER.
+chown -R ${SYSTEM_USER}:${SYSTEM_USER} /opt/aiida-raspa/
diff --git a/.docker/opt/add-codes.sh b/.docker/opt/add-codes.sh
@@ -8,7 +8,18 @@ set -x
 # Environment
 export SHELL=/bin/bash
 
-# Install the ddec and cp2k codes
-RASPA_FOLDER=/home/aiida/code/aiida-raspa
+# Activate conda.
+__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
+        . "/opt/conda/etc/profile.d/conda.sh"
+    else
+        export PATH="/opt/conda/bin:$PATH"
+    fi
+fi
+unset __conda_setup
 
-verdi code show raspa@localhost || verdi code setup --config ${RASPA_FOLDER}/.docker/raspa-code.yml --non-interactive
+# Install raspa code.
+verdi code show raspa@localhost || verdi code setup --config /opt/aiida-raspa/.docker/raspa-code.yml --non-interactive
diff --git a/.docker/raspa-code.yml b/.docker/raspa-code.yml
@@ -3,6 +3,6 @@ computer: localhost
 description:
 input_plugin: raspa
 on_computer: True
-remote_abs_path: /home/aiida/code/RASPA2_installed/bin/simulate
+remote_abs_path: /opt/RASPA2_installed/bin/simulate
 append_text:
-prepend_text: export RASPA2_DIR=/home/aiida/code/RASPA2_installed/
+prepend_text: export RASPA2_DIR=/opt/RASPA2_installed/
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,7 @@
+build:
+  image: latest
+python:
+  version: 3.6
+  pip_install: true
+  extra_requirements:
+  - "docs"
diff --git a/.travis.yml b/.travis.yml
@@ -6,17 +6,20 @@ services:
 before_install:
   - python .ci/check_travis_tag.py
   - docker build -t aiida_raspa_test .
-  - docker run -d aiida_raspa_test
-  - sleep 30 # wait untill the container is launched
+  - export DOCKERID=`docker run -d aiida_raspa_test`
 
 script:
-  - "export DOCKERID=`docker ps -qf 'ancestor=aiida_raspa_test'`"
+  - docker exec --tty $DOCKERID wait-for-services
   - "echo \"Docker ID: $DOCKERID\""
-  - "docker exec -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-raspa/ && pre-commit run --all-files || ( git status --short ; git diff ; exit 1 ) '"
-  - "docker exec -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-raspa/ && py.test --cov aiida_raspa --cov-append .'"
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-raspa/ && pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )'
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-raspa/ && py.test --cov aiida_raspa --cov-append .'
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-raspa/docs && make'
 
 after_success:
-  - "docker exec -e TRAVIS=\"$TRAVIS\" -e TRAVIS_JOB_ID=\"$TRAVIS_JOB_ID\" -e TRAVIS_BRANCH=\"$TRAVIS_BRANCH\" -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-raspa/ && coveralls'"
+  - docker exec -e TRAVIS=$TRAVIS -e TRAVIS_JOB_ID=$TRAVIS_JOB_ID -e TRAVIS_BRANCH=$TRAVIS_BRANCH -it --user aiida $DOCKERID /bin/bash -l -c 'cd code/aiida-raspa/ && coveralls'
+
+after_script:
+  - docker logs $DOCKERID
 
 git:
   depth: 3
diff --git a/Dockerfile b/Dockerfile
@@ -1,26 +1,28 @@
-FROM aiidateam/aiida-docker-stack
+FROM aiidateam/aiida-core:latest
 
 # Set HOME, PATH and RASPA_DIR variables:
-ENV HOME="/home/aiida"
-ENV RASPA2_DIR=${HOME}/code/RASPA2_installed
-ENV PATH="/home/aiida/code/RASPA2_installed/bin/:${HOME}/.local/bin:${PATH}"
+ENV PATH="/opt/RASPA2_installed/bin/:${PATH}"
+ENV RASPA2_DIR=/opt/RASPA2_installed
+ENV KILL_ALL_RPOCESSES_TIMEOUT=50
 
-# Install necessary codes to build RASPA
-RUN apt-get update && apt-get install -y --no-install-recommends  \
+WORKDIR /opt/
+
+# Copy and install aiida-raspa plugin.
+COPY . aiida-raspa
+RUN pip install ./aiida-raspa[pre-commit,test,docs]
+
+# Install coveralls.
+RUN pip install coveralls
+
+# Install necessary codes to build RASPA2.
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* && apt-get update && apt-get install -y --no-install-recommends  \
     automake \
     libtool
 
-# Copy the current folder and change permissions
-COPY . ${HOME}/code/aiida-raspa
-RUN chown -R aiida:aiida ${HOME}/code
 
-# Now do everything as the aiida user
-USER aiida
-
-# Download, compile and install RASPA into ~/code folder
-WORKDIR ${HOME}/code/
+# Download, compile and install RASPA into ~/code folder.
 RUN git clone https://github.com/iRASPA/RASPA2.git RASPA2
-WORKDIR ${HOME}/code/RASPA2
+WORKDIR /opt/RASPA2
 RUN rm -rf autom4te.cache
 RUN mkdir m4
 RUN aclocal
@@ -31,25 +33,6 @@ RUN ./configure --prefix=${RASPA2_DIR}
 RUN make
 RUN make install
 
-# Set the plugin folder as the workdir
-WORKDIR ${HOME}/code/aiida-raspa
-
-# Install aiida-raspa plugin and coveralls
-RUN pip install --user .[pre-commit,test]
-RUN pip install --user coveralls
-
-# Populate reentry cache for aiida user https://pypi.python.org/pypi/reentry/
-RUN reentry scan
-
-# Install the RASPA code to AiiDA
+# Install the RASPA code to AiiDA.
 COPY .docker/opt/add-codes.sh /opt/
-COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/40_add-codes.sh
-
-# Change workdir back to $HOME
-WORKDIR ${HOME}
-
-# Important to end as user root!
-USER root
-
-# Use baseimage-docker's init system.
-CMD ["/sbin/my_init"]
+COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/50_add-codes.sh
diff --git a/README.md b/README.md
@@ -2,201 +2,63 @@
 [![Coverage Status](https://coveralls.io/repos/github/yakutovicha/aiida-raspa/badge.svg?branch=develop)](https://coveralls.io/github/yakutovicha/aiida-raspa?branch=develop)
 [![PyPI version](https://badge.fury.io/py/aiida-raspa.svg)](https://badge.fury.io/py/aiida-raspa)
 
-# aiida-raspa
-
+# AiiDA RASPA
 [AiiDA](http://www.aiida.net/) plugin for [RASPA2](https://github.com/iRASPA/RASPA2).
 
-## Installation
+Designed to work with with RASPA 2.0.37 or later.
+
+# Documentation
+The documentation for this package can be found on [Read the Docs](https://aiida-raspa.readthedocs.io/en/latest/).
+
 
+# Installation
 If you use ``pip``, you can install it as:
 ```
 pip install aiida-raspa
 ```
+
 If you want to install the plugin in an editable mode, run:
 ```
 git clone https://github.com/yakutovicha/aiida-raspa
 cd aiida-raspa
-pip install -e .  # also installs aiida, if missing (but not postgres)
-```
-In case the plugin does not appear in `verdi calculation plugins` list, run 
-```
-reentry scan
+pip install -e .  # Also installs aiida, if missing (but not postgres/rabbitmq).
 ```
-and try again.
 
+In case the plugin does not appear in the output of `verdi plugin list aiida.calculations`,
+run `reentry scan` and try again.
 
-## Examples
 
-See `examples` folder for complete examples of setting up a calculation or workflow.
+# Examples
+See `examples` folder for complete examples of setting up a calculation or a work chain.
 
-simple calculation:
+## Simple calculation
 ```shell
-verdi daemon restart                                   # make sure the daemon is running
 cd examples/simple_calculations
-verdi run test_raspa_base.py <code_label> --submit     # submit test calculation
-verdi calculation list -a -p1                          # check status of calculation
-```
-workflow:
-```shell
-verdi daemon restart                                   # make sure the daemon is running
-cd examples/workflows
-verdi run run_RaspaConverge_workflow.py  <code_label>  # submit test calculation
-verdi work list -a -p1                                 # check status of calculation
-```
-
-## Analyzing output
-```shell
-$ verdi calculation show 7491
------------  ------------------------------------
-type         RaspaCalculation
-pk           7491
-uuid         adc178d9-9f7e-4bbf-8283-8768f1964d9a
-label
-description
-ctime        2019-01-10 15:38:20.103794+00:00
-mtime        2019-01-10 15:39:24.799300+00:00
-computer     [3] deneb
-code         raspa
------------  ------------------------------------
-##### INPUTS:
-Link label      PK  Type
-------------  ----  -------------
-parameters    7490  ParameterData
-structure     7489  CifData
-##### OUTPUTS:
-Link label           PK  Type
------------------  ----  -------------
-remote_folder      7492  RemoteData
-retrieved          7498  FolderData
-output_parameters  7499  ParameterData
-component_0        7500  ParameterData
-```
-Results that are for the framework and adsorbate can be obtained:
-```shell
-$ verdi calculation res 7491 # same as $ verdi data parameter show 7499
-{
-  "ads_ads_coulomb_energy_average": 0.0, 
-  "ads_ads_coulomb_energy_dev": 0.0, 
-  "ads_ads_coulomb_energy_unit": "kJ/mol", 
-  "ads_ads_total_energy_average": -4.4408682910929, 
-  "ads_ads_total_energy_dev": 1.63152616602518, 
-  "ads_ads_total_energy_unit": "kJ/mol", 
-  "ads_ads_vdw_energy_average": -4.44086832435076, 
-  "ads_ads_vdw_energy_dev": 1.63152614939625, 
-  "ads_ads_vdw_energy_unit": "kJ/mol", 
-  "adsorbate_density_average": 26.35203, 
-  "adsorbate_density_dev": 4.63163, 
-  "adsorbate_density_unit": "kg/m^3", 
-  "cell_volume_average": 12025.61229, 
-  "cell_volume_dev": 0.0, 
-  "cell_volume_unit": "A^3", 
-  "enthalpy_of_adsorption_average": -2092.24759, 
-  "enthalpy_of_adsorption_dev": 315.039138, 
-  "enthalpy_of_adsorption_unit": "K", 
-  "exceeded_walltime": false, 
-  "framework_density": "739.995779685958", 
-  "framework_density_unit": "kg/m^3", 
-  "framework_heat_capacity_average": 3082.15209, 
-  "framework_heat_capacity_dev": 2889.16503, 
-  "framework_heat_capacity_unit": "J/mol/K", 
-  "host_ads_coulomb_energy_average": 0.0, 
-  "host_ads_coulomb_energy_dev": 0.0, 
-  "host_ads_coulomb_energy_unit": "kJ/mol", 
-  "host_ads_total_energy_average": -176.211538447682, 
-  "host_ads_total_energy_dev": 36.0785945303337, 
-  "host_ads_total_energy_unit": "kJ/mol", 
-  "host_ads_vdw_energy_average": -176.211538455997, 
-  "host_ads_vdw_energy_dev": 36.0785944970758, 
-  "host_ads_vdw_energy_unit": "kJ/mol", 
-  "pressure_average": 0.0, 
-  "pressure_dev": 0.0, 
-  "pressure_unit": "Pa", 
-  "temperature_average": 0.0, 
-  "temperature_dev": 0.0, 
-  "temperature_unit": "K", 
-  "total_energy_average": -21727.4844, 
-  "total_energy_dev": 4526.71327, 
-  "total_energy_unit": "K"
-}
-```
-Component specific results can be obtained:
-```shell
-$ verdi data parameter show 7499
-{
-  "ads_ads_coulomb_energy_average": 0.0, 
-  "ads_ads_coulomb_energy_dev": 0.0, 
-  "ads_ads_coulomb_energy_unit": "kJ/mol", 
-  "ads_ads_total_energy_average": -4.4408682910929, 
-  "ads_ads_total_energy_dev": 1.63152616602518, 
-  "ads_ads_total_energy_unit": "kJ/mol", 
-  "ads_ads_vdw_energy_average": -4.44086832435076, 
-  "ads_ads_vdw_energy_dev": 1.63152614939625, 
-  "ads_ads_vdw_energy_unit": "kJ/mol", 
-  "adsorbate_density_average": 26.35203, 
-  "adsorbate_density_dev": 4.63163, 
-  "adsorbate_density_unit": "kg/m^3", 
-  "cell_volume_average": 12025.61229, 
-  "cell_volume_dev": 0.0, 
-  "cell_volume_unit": "A^3", 
-  "enthalpy_of_adsorption_average": -2092.24759, 
-  "enthalpy_of_adsorption_dev": 315.039138, 
-  "enthalpy_of_adsorption_unit": "K", 
-  "exceeded_walltime": false, 
-  "framework_density": "739.995779685958", 
-  "framework_density_unit": "kg/m^3", 
-  "framework_heat_capacity_average": 3082.15209, 
-  "framework_heat_capacity_dev": 2889.16503, 
-  "framework_heat_capacity_unit": "J/mol/K", 
-  "host_ads_coulomb_energy_average": 0.0, 
-  "host_ads_coulomb_energy_dev": 0.0, 
-  "host_ads_coulomb_energy_unit": "kJ/mol", 
-  "host_ads_total_energy_average": -176.211538447682, 
-  "host_ads_total_energy_dev": 36.0785945303337, 
-  "host_ads_total_energy_unit": "kJ/mol", 
-  "host_ads_vdw_energy_average": -176.211538455997, 
-  "host_ads_vdw_energy_dev": 36.0785944970758, 
-  "host_ads_vdw_energy_unit": "kJ/mol", 
-  "pressure_average": 0.0, 
-  "pressure_dev": 0.0, 
-  "pressure_unit": "Pa", 
-  "temperature_average": 0.0, 
-  "temperature_dev": 0.0, 
-  "temperature_unit": "K", 
-  "total_energy_average": -21727.4844, 
-  "total_energy_dev": 4526.71327, 
-  "total_energy_unit": "K"
-}
+verdi run example_base.py <code_label> --submit          # Submit example calculation.
+verdi process list -a -p1                                # Check status of calculation.
 ```
 
-Files that are downloaded by the plugin to the local machine:
+## Work chain
 ```shell
-$ verdi calculation outputls 7491
-_scheduler-stderr.txt
-_scheduler-stdout.txt
-output_framework_1.1.1_300.000000_500000.data
-restart_framework_1.1.1_300.000000_500000
+cd examples/workchains
+verdi run example_base_restart_timeout.py  <code_label>  # Submit test calculation.
+verdi process list -a -p1                                # Check status of the work chain.
 ```
 
-Cat the output file:
-```shell
-$ verdi calculation outputcat 7491 -p output_framework_1.1.1_300.000000_500000.data
-...
-Average adsorption energy <U_gh>_1-<U_h>_0 obtained from Widom-insertion:
-(Note: the total heat of adsorption is dH=<U_gh>_1-<U_h>_0 - <U_g> - RT)
-=========================================================================
-
-Simulation finished,  1 warnings
-WARNING: INAPPROPRIATE NUMBER OF UNIT CELLS USED
 
+# License
+MIT
 
-Thu Jan 10 16:39:01 2019
-Simulation finished on Thursday, January 10.
-The end time was 04:39 PM.
-```
+# Contact
+yakutovicha@gmail.com
 
-## License
 
-MIT
+# 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;
+* the [swissuniversities P-5 project "Materials Cloud"](https://www.materialscloud.org/swissuniversities).
 
-## Contact
-yakutovicha@gmail.com
+<img src="miscellaneous/logos/MARVEL.png" alt="MARVEL" style="padding:10px;" width="150"/>
+<img src="miscellaneous/logos/MaX.png" alt="MaX" style="padding:10px;" width="250"/>
+<img src="miscellaneous/logos/swissuniversities.png" alt="swissuniversities" style="padding:10px;" width="250"/>
diff --git a/aiida_raspa/__init__.py b/aiida_raspa/__init__.py
@@ -9,4 +9,4 @@
 ##############################################################################
 """AiiDA-RASPA plugins, parsers, workflows, etc ..."""
 
-__version__ = "1.0.0a3"
+__version__ = "1.0.0"