Merge pull request #297 from choderalab/fix-warnings

Fix warnings with bondtype

.github/workflows/CI.yaml

@@ -0,0 +1,116 @@
+name: CI
+
+on:
+  pull_request:
+  schedule:
+    # nightly tests
+    - cron: '0 0 * * *'
+
+jobs:
+  test:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        cfg:
+          - {python-version: 3.6, openmm: "latest"}
+          - {python-version: 3.7, openmm: "latest"}
+          - {python-version: 3.7, openmm: "beta"}
+          - {python-version: 3.7, openmm: "nightly"}
+          - {python-version: 3.7, openmm: "conda-forge"}
+
+    env:
+      ORGNAME: omnia
+      PACKAGENAME: openmoltools
+      OE_LICENSE: $HOME/oe_license.txt
+      CI_OS: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+    - name: Configure conda
+      shell: bash
+      run: |
+        . devtools/github-actions/initialize_conda.sh
+        conda activate
+        conda config --set always_yes True
+        conda config --add channels conda-forge
+        conda config --add channels omnia
+        conda config --add channels openeye
+        conda update --quiet --all
+        conda install --quiet conda conda-build jinja2 anaconda-client
+        conda info
+        conda list
+    - name: Decrypt OpenEye license
+      shell: bash
+      env:
+        ENC_OE_LICENSE: ${{ secrets.ENC_OE_LICENSE }}
+      run: |
+        echo "${ENC_OE_LICENSE}" > $HOME/oe_license.txt
+
+    - name: Create environment for package
+      shell: bash
+      run: |
+        . devtools/github-actions/initialize_conda.sh
+        conda activate
+        conda info
+        python devtools/scripts/create_conda_env.py -n=test -p=$PYVER devtools/conda-envs/test_env.yaml
+
+    - name: Install package
+      shell: bash
+      run: |
+        . devtools/github-actions/initialize_conda.sh
+        conda activate test
+        python -m pip install . --no-deps
+        conda list --show-channel-urls
+
+    - name: Prepare test environment
+      shell: bash
+      run: |
+        . devtools/github-actions/initialize_conda.sh
+        conda activate test
+        case ${{ matrix.cfg.openmm }} in
+          latest)
+            echo "Using latest release OpenMM."
+            conda install --quiet -c omnia openmm;;
+          beta)
+            echo "Using OpenMM beta"
+            conda install --quiet -c omnia/label/beta openmm;;
+          nightly)
+            echo "Using OpenMM nightly dev build."
+            conda install --quiet -c omnia-dev openmm;;
+          conda-forge)
+            echo "Using OpenMM conda-forge testing build."
+            conda install --quiet -c conda-forge/label/testing openmm;;
+        esac
+
+    - name: Test the package
+      shell: bash
+      run: |
+        . devtools/github-actions/initialize_conda.sh
+        conda activate test
+        export OE_LICENSE="$HOME/oe_license.txt"
+        export TRAVIS=true
+        pushd .
+        nosetests ${PACKAGENAME}/tests/test_forcefield_generators.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_amber.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_utils.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_gromacs.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_openeye.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_freesolv.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_drugs.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        nosetests ${PACKAGENAME}/tests/test_common_molecules.py --nocapture --verbosity=3 --with-timer -a '!advanced'
+        popd
+
+    - name: Deploy
+      shell: bash
+      if: false
+      run: |
+        echo "Deployment has not been implemented yet"

README.md

@@ -1,4 +1,5 @@
 [![Build Status](https://travis-ci.org/choderalab/openmoltools.svg?branch=master)](https://travis-ci.org/choderalab/openmoltools)
+[![GH Actions Status](https://github.com/choderalab/perses/workflows/CI/badge.svg)](https://github.com/choderalab/perses/actions?query=branch%3Amaster)
 
 ## openmoltools: Tools for Small Molecules, Antechamber, OpenMM, and More.
 
@@ -40,8 +41,7 @@ nosetests openmoltools -v --exe
 ## Python 2.7 builds are deprecated
 
 Version 0.8.3 will be the last version of this package to build with Python 2.7.
-With the OpenEye toolkits no longer being depolyed on Python 2.7 as of 2018.2.1, 
-we have decided to deprecate support for that Python version as well. 
-Version 0.8.3 was tested against the 2017.10.1 version of the OpenEye Toolkits for 
+With the OpenEye toolkits no longer being depolyed on Python 2.7 as of 2018.2.1,
+we have decided to deprecate support for that Python version as well.
+Version 0.8.3 was tested against the 2017.10.1 version of the OpenEye Toolkits for
 compatibility.
-

devtools/conda-envs/test_env.yaml

@@ -0,0 +1,34 @@
+name: test
+channels:
+  - conda-forge
+  - omnia
+  - openeye
+dependencies:
+    # Base depends
+  - python
+  - pip
+  - setuptools
+  - pandas
+  - six
+  - mdtraj
+  - lxml
+  - pymbar
+  - numpy
+  - numpydoc
+  - scipy
+  - openmm
+  - ambertools >=19.0
+  - pytables
+  - openmmtools
+  - packmol
+  - rdkit    # optional dependency
+  - openeye-toolkits  # optional dependency
+
+    # Testing
+  - nose
+  - nose-timer
+  - pytest
+  - pytest-cov
+  # Pip-only installs
+  - pip:
+    - codecov

devtools/conda-recipe/meta.yaml

@@ -16,14 +16,18 @@ requirements:
     - pandas
     - six
     - mdtraj
+    - lxml
+    - pymbar
     - numpy
     - numpydoc
     - scipy
     - openmm
-    - ambermini
+    - ambertools >=19
     - pytables
-    - parmed
-    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
+    - openmmtools
+    - packmol
+    - rdkit    # optional dependency
+    - openeye-toolkits  # optional dependency
   run:
     - python
     - setuptools
@@ -36,15 +40,16 @@ requirements:
     - numpydoc
     - scipy
     - openmm
-    - ambermini
+    - ambertools >=19
     - pytables
-    - parmed
-    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
+    - openmmtools
+    - packmol
+    - rdkit    # optional dependency
+    - openeye-toolkits  # optional dependency
 
 test:
   requires:
     - nose
-    - openmmtools
   imports:
     - openmoltools
   #commands:

devtools/github-actions/initialize_conda.sh

@@ -0,0 +1,8 @@
+# $CI_OS is $matrix.os, as exported in GHA *.yaml
+# $CONDA (miniconda installation path) is always defined in the GHA virtual environments
+case ${CI_OS} in
+    windows*)
+        eval "$(${CONDA}/condabin/conda.bat shell.bash hook)";;
+    *)
+        eval "$(${CONDA}/condabin/conda shell.bash hook)";;
+esac

devtools/scripts/create_conda_env.py

@@ -0,0 +1,95 @@
+import argparse
+import os
+import re
+import glob
+import shutil
+import subprocess as sp
+from tempfile import TemporaryDirectory
+from contextlib import contextmanager
+# YAML imports
+try:
+    import yaml  # PyYAML
+    loader = yaml.load
+except ImportError:
+    try:
+        import ruamel_yaml as yaml  # Ruamel YAML
+    except ImportError:
+        try:
+            # Load Ruamel YAML from the base conda environment
+            from importlib import util as import_util
+            CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE'])
+            ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..',
+                                                      'lib', 'python*.*', 'site-packages',
+                                                      'ruamel_yaml', '__init__.py'))[0]
+            # Based on importlib example, but only needs to load_module since its the whole package, not just
+            # a module
+            spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path)
+            yaml = spec.loader.load_module()
+        except (KeyError, ImportError, IndexError):
+            raise ImportError("No YAML parser could be found in this or the conda environment. "
+                              "Could not find PyYAML or Ruamel YAML in the current environment, "
+                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
+                              "Environment not created!")
+    loader = yaml.YAML(typ="safe").load  # typ="safe" avoids odd typing on output
+
+
+@contextmanager
+def temp_cd():
+    """Temporary CD Helper"""
+    cwd = os.getcwd()
+    with TemporaryDirectory() as td:
+        try:
+            os.chdir(td)
+            yield
+        finally:
+            os.chdir(cwd)
+
+
+# Args
+parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
+parser.add_argument('-n', '--name', type=str,
+                    help='The name of the created Python environment')
+parser.add_argument('-p', '--python', type=str,
+                    help='The version of the created Python environment')
+parser.add_argument('conda_file',
+                    help='The file for the created Python environment')
+
+args = parser.parse_args()
+
+# Open the base file
+with open(args.conda_file, "r") as handle:
+    yaml_script = loader(handle.read())
+
+python_replacement_string = "python {}*".format(args.python)
+
+try:
+    for dep_index, dep_value in enumerate(yaml_script['dependencies']):
+        if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value):  # Match explicitly 'python' and its formats
+            yaml_script['dependencies'].pop(dep_index)
+            break  # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
+except (KeyError, TypeError):
+    # Case of no dependencies key, or dependencies: None
+    yaml_script['dependencies'] = []
+finally:
+    # Ensure the python version is added in. Even if the code does not need it, we assume the env does
+    yaml_script['dependencies'].insert(0, python_replacement_string)
+
+# Figure out conda path
+if "CONDA_EXE" in os.environ:
+    conda_path = os.environ["CONDA_EXE"]
+else:
+    conda_path = shutil.which("conda")
+if conda_path is None:
+    raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path")
+
+print("CONDA ENV NAME  {}".format(args.name))
+print("PYTHON VERSION  {}".format(args.python))
+print("CONDA FILE NAME {}".format(args.conda_file))
+print("CONDA PATH      {}".format(conda_path))
+
+# Write to a temp directory which will always be cleaned up
+with temp_cd():
+    temp_file_name = "temp_script.yaml"
+    with open(temp_file_name, 'w') as f:
+        f.write(yaml.dump(yaml_script))
+    sp.call("{} env create --quiet -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True)