diff --git a/.circleci/config.yml b/.circleci/config.yml index 2c883980..51fa32f0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,8 +4,6 @@ jobs: test: docker: - image: cimg/python:<> - environment: - PYTHON_VERSION: "<>" parameters: python-version: type: string @@ -61,17 +59,20 @@ jobs: - run: name: Run unit tests + # no_output_timeout: 1h command: | source $HOME/pkgs/bin/GMXRC pip3 install pytest pip3 install pytest-mpi pip3 install pytest-cov + + # sleep 3000 # only for debugging purposes coverage run -m pytest -vv --disable-pytest-warnings --color=yes ensemble_md/tests - mpirun -np 4 coverage run --rcfile setup.cfg -m pytest ensemble_md/tests/test_mpi_func.py --with-mpi -vv --disable-pytest-warnings --color=yes # this will generate multiple .coverage* files that can be combined - coverage combine # This will combine multiple .coverage* files into a single .coverage file that will be uploaded and reported. + # mpirun -np 4 coverage run --rcfile setup.cfg -m pytest ensemble_md/tests/test_mpi_func.py --with-mpi -vv --disable-pytest-warnings --color=yes # this will generate multiple .coverage* files that can be combined + # coverage combine # This will combine multiple .coverage* files into a single .coverage file that will be uploaded and reported. - # Below are some old commands: + # Another section of old commands # pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/ # COVERAGE_FILE=.coverage_1 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/ # COVERAGE_FILE=.coverage_2 mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/test_mpi_func.py --with-mpi @@ -88,12 +89,6 @@ jobs: workflows: continuous-integration: jobs: - - test: - name: test-python-3.8 - python-version: "3.8" - # - test: - # name: test-python-3.9 - # python-version: "3.9" - test: name: test-python-3.10 python-version: "3.10" diff --git a/docs/examples/tutorial_1/standard_REXEE.ipynb b/docs/examples/tutorial_1/standard_REXEE.ipynb index d0395e39..11a7611c 100644 --- a/docs/examples/tutorial_1/standard_REXEE.ipynb +++ b/docs/examples/tutorial_1/standard_REXEE.ipynb @@ -13,7 +13,7 @@ "id": "48c42ec7", "metadata": {}, "source": [ - "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/wehs7661/ensemble_md/c0f6d48ce3fe746e349e4a4a9610f935cca8b0b5?urlpath=lab%2Ftree%2Fdocs%2Fexamples%2Ftutorial_1%2Frun_REXEE.ipynb)\n", + "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/wehs7661/ensemble_md.git/HEAD?labpath=docs%2Fexamples%2Ftutorial_1%2Fstandard_REXEE.ipynb)\n", "\n", "In this tutorial, we will demonstrate how one can use the different command-line interfaces (CLIs) implemented in the Python package `ensemble_md` to prepare, perform, and analyze a REXEE simulation to estimate the solvation free energy of a toy molecule composed of 4 interaction sites. For a more comprehensive understanding, we strongly recommend reading our [documentation](https://ensemble-md.readthedocs.io/en/latest/simulations.html) on launching REXEE simulations before starting this tutorial. For the theory behind the REXEE method, we recommend reading our [JCTC paper](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00494) or the [theory section](https://ensemble-md.readthedocs.io/en/add_tutorials/theory.html) of our documentation.\n", "\n", @@ -1093,8 +1093,6 @@ "id": "4378660a-e52c-4fac-acbd-6269b6fe2a1f", "metadata": {}, "source": [ - "
\n", - "\n", "### 4.1. Replica-space sampling\n", "As shown in the replica-space trajectories in the left figure below, each replica was able to sample all different sets of states by exchanging coordinates with other replicas, indicating good sampling in the replica space. This decent sampling in the replica space is also reflected in the replica-space transition matrix in the right figure, where all tridiagonal elements are non-zero. " ] diff --git a/ensemble_md/tests/test_replica_exchange_EE.py b/ensemble_md/tests/test_replica_exchange_EE.py index 61ea5bdf..6a19f7fe 100644 --- a/ensemble_md/tests/test_replica_exchange_EE.py +++ b/ensemble_md/tests/test_replica_exchange_EE.py @@ -25,6 +25,9 @@ from ensemble_md.replica_exchange_EE import ReplicaExchangeEE from ensemble_md.utils.exceptions import ParameterError +import logging +logging.basicConfig(level=logging.DEBUG) + current_path = os.path.dirname(os.path.abspath(__file__)) input_path = os.path.join(current_path, "data") @@ -74,8 +77,10 @@ def check_param_error(REXEE_dict, param, match, wrong_val='cool', right_val=None class Test_ReplicaExchangeEE: def test_init(self, params_dict): + logging.debug("Initializing ReplicaExchangeEE") REXEE = get_REXEE_instance(params_dict) assert REXEE.yaml == 'params.yaml' + logging.debug("Finished initializing ReplicaExchangeEE") def test_set_params_error(self, params_dict): # 1. Required parameters