Move tests to the pytest framework, add badges(#34)

fixes #28
fixes #29
fixes #31

* Rename all examples from `text_` to `example_`
* Add `check_travis_tag.py` test
* Make all tests run by pytest
* Compute test coverage and submit to coveralls
* Add Travis and coveralls badges
* Skip binary restart test for the moment, as it is hanging (see the issue #40)
* Reorder a bit the Docker file, make it more clear
* Move supplementary files from `examples/simple_calculations` to `examples`

.ci/check_travis_tag.py

@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+# pylint: disable=invalid-name
+###############################################################################
+# Copyright (c), The AiiDA-CP2K authors.                                      #
+# SPDX-License-Identifier: MIT                                                #
+# AiiDA-CP2K is hosted on GitHub at https://github.com/aiidateam/aiida-cp2k   #
+# For further information on the license, see the LICENSE.txt file.           #
+###############################################################################
+"""Check travis tag"""
+from __future__ import print_function
+from __future__ import absolute_import
+
+import os
+import sys
+import json
+
+a = os.getenv("TRAVIS_TAG")
+with open("setup.json") as fhandle:
+    b = "v{version}".format(**json.load(fhandle))
+
+if not a:
+    print("TRAVIS_TAG not set")
+
+elif a != b:
+    print("ERROR: TRAVIS_TAG and version are inconsistent: '{}' vs '{}'".format(a, b))
+    sys.exit(3)

.travis.yml

@@ -4,14 +4,19 @@ services:
 - docker
 
 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
 
 script:
-  - sleep 30 # wait untill the container is launched
   - "export DOCKERID=`docker ps -qf 'ancestor=aiida_raspa_test'`"
   - "echo \"Docker ID: $DOCKERID\""
-  - "docker exec -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-raspa/ && ./run_tests.sh'"
+  - "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 .'"
+
+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'"
 
 git:
   depth: 3

Dockerfile

@@ -1,30 +1,23 @@
 FROM aiidateam/aiida-docker-stack
 
-# Set HOME variable:
+# 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}"
 
-# Install necessary codes 
+# Install necessary codes to build RASPA
 RUN 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
 
-# Change user to aiida
+# Now do everything as the aiida user
 USER aiida
 
-# Install aiida-raspa plugin and it's dependencies
-WORKDIR ${HOME}/code/aiida-raspa
-RUN pip install --user .[pre-commit,test]
-
-# Install AiiDA
-ENV PATH="${HOME}/.local/bin:${PATH}"
-
-# Download, compile and install RASPA
+# Download, compile and install RASPA into ~/code folder
 WORKDIR ${HOME}/code/
 RUN git clone https://github.com/iRASPA/RASPA2.git RASPA2
 WORKDIR ${HOME}/code/RASPA2
@@ -38,10 +31,17 @@ RUN ./configure --prefix=${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 ddec and cp2k codes
+# 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
 

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/yakutovicha/aiida-raspa.svg?branch=develop)](https://travis-ci.org/yakutovicha/aiida-raspa)
+[![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

conftest.py

@@ -0,0 +1,11 @@
+"""
+For pytest initialise a test database and profile
+"""
+from __future__ import absolute_import
+import pytest
+pytest_plugins = ['aiida.manage.tests.pytest_fixtures']  # pylint: disable=invalid-name
+
+
+@pytest.fixture(scope='function')
+def raspa_code(aiida_local_code_factory):  # pylint: disable=unused-argument
+    return aiida_local_code_factory("raspa", "simulate")

examples/simple_calculations/test_base.py → examples/simple_calculations/example_base.py

@@ -6,6 +6,7 @@
 import os
 import sys
 import click
+import pytest
 
 from aiida.common import NotExistent
 from aiida.engine import run_get_pk, run
@@ -16,16 +17,8 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_base(raspa_code, submit=True):
     """Prepare and submit simple RASPA calculation."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -61,10 +54,10 @@ def main(codelabel, submit):
         })
 
     # framework
-    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'files', 'TCC1RS.cif'))
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "tcc1rs": framework,
     }
@@ -86,6 +79,7 @@ def main(codelabel, submit):
         print("calculation pk: ", pk)
         print("Total Energy average (tcc1rs):", res['output_parameters'].dict.tcc1rs['general']['total_energy_average'])
         print("OK, calculation has completed successfully")
+        pytest.base_calc_pk = pk
     else:
         print("Generating test input ...")
         builder.metadata.dry_run = True
@@ -96,7 +90,20 @@ def main(codelabel, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_base(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_restart.py → examples/simple_calculations/example_base_restart.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python2
 # -*- coding: utf-8 -*-
 """Restart from simple RASPA calculation."""
 
@@ -7,6 +6,7 @@
 import os
 import sys
 import click
+import pytest
 
 from aiida.common import NotExistent
 from aiida.engine import run_get_pk, run
@@ -17,17 +17,12 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--previous_calc', '-p', required=True, type=int, help='PK of test_raspa_base.py calculation')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, previous_calc, submit):
+def example_base_restart(raspa_code, base_calc_pk=None, submit=True):
     """Prepare and submit restart from simple RASPA calculation."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
+
+    # This line is needed for tests only
+    if base_calc_pk is None:
+        base_calc_pk = pytest.base_calc_pk  # pylint: disable=no-member
 
     # parameters
     parameters = Dict(
@@ -62,13 +57,13 @@ def main(codelabel, previous_calc, submit):
         })
 
     # framework
-    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'files', 'TCC1RS.cif'))
 
     # restart file
-    retrieved_parent_folder = load_node(previous_calc).outputs.retrieved
+    retrieved_parent_folder = load_node(base_calc_pk).outputs.retrieved
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "tcc1rs": framework,
     }
@@ -101,7 +96,21 @@ def main(codelabel, previous_calc, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--previous_calc', '-p', required=True, type=int, help='PK of example_base.py calculation')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, previous_calc, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_base_restart(code, previous_calc, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_binary_mixture.py → examples/simple_calculations/example_binary_mixture.py

@@ -11,16 +11,8 @@
 from aiida.orm import Code, Dict
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_binary_misture(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with components mixture."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -63,7 +55,7 @@ def main(codelabel, submit):
         })
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.parameters = parameters
     builder.metadata.options = {
         "resources": {
@@ -93,7 +85,20 @@ def main(codelabel, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_binary_misture(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_block_pockets_2frameworks_2molecules.py → examples/simple_calculations/example_block_pockets_2frameworks_2molecules.py

@@ -15,16 +15,9 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_block_pockets(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with blocked pockets."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
+
     # parameters
     parameters = Dict(
         dict={
@@ -88,15 +81,15 @@ def main(codelabel, submit):
 
     # frameworks
     pwd = os.path.dirname(os.path.realpath(__file__))
-    framework_1 = CifData(file=os.path.join(pwd, 'files', 'IRMOF-1.cif'))
-    framework_10 = CifData(file=os.path.join(pwd, 'files', 'IRMOF-10.cif'))
+    framework_1 = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1.cif'))
+    framework_10 = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-10.cif'))
 
     # block pocket
-    block_pocket_1 = SinglefileData(file=os.path.join(pwd, 'files', 'IRMOF-1_test.block')).store()
-    block_pocket_10 = SinglefileData(file=os.path.join(pwd, 'files', 'IRMOF-10_test.block')).store()
+    block_pocket_1 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1_test.block')).store()
+    block_pocket_10 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'IRMOF-10_test.block')).store()
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "irmof_1": framework_1,
         "irmof_10": framework_10,
@@ -136,7 +129,20 @@ def main(codelabel, submit):
         print("In order to actually submit, add '--submit'")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_block_pockets(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF