Merge pull request #54 from wehs7661/final_tweaks

Final tweaks before releasing version 1.0.0

Author: weitse-hsu

.circleci/config.yml

@@ -4,8 +4,6 @@ jobs:
   test:
     docker:
       - image: cimg/python:<<parameters.python-version>>
-    environment:
-      PYTHON_VERSION: "<<parameters.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"

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": [
-    "</br>\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. "
    ]

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