diff --git a/.gitignore b/.gitignore index eea1cc840..588bf8444 100644 --- a/.gitignore +++ b/.gitignore @@ -142,3 +142,6 @@ cython_debug/ # IDEs .idea/ .vscode/ + +# SonarQube +.scannerwork/ diff --git a/devtools/travis-ci/after_success.sh b/devtools/travis-ci/after_success.sh deleted file mode 100755 index 0b0003fea..000000000 --- a/devtools/travis-ci/after_success.sh +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/bash -# Must be invoked with $PACKAGENAME - -echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH -PUSH_DOCS_TO_S3=false - -if [ "$TRAVIS_PULL_REQUEST" = true ]; then - echo "This is a pull request. No deployment will be done."; exit 0 -fi - - -if [ "$TRAVIS_BRANCH" != "master" ]; then - echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0 -fi - - -# Deploy to binstar -conda install --yes anaconda-client jinja2 -#binstar -t $BINSTAR_TOKEN upload --force -u ${ORGNAME} -p ${PACKAGENAME}-dev $HOME/miniconda/conda-bld/*/${PACKAGENAME}-dev-*.tar.bz2 - -if [ $PUSH_DOCS_TO_S3 = true ]; then - # Create the docs and push them to S3 - # ----------------------------------- - conda install --yes pip - conda config --add channels http://conda.binstar.org/omnia - conda install --yes `conda build devtools/conda-recipe --output` - pip install numpydoc s3cmd msmb_theme - conda install --yes `cat docs/requirements.txt | xargs` - - conda list -e - - (cd docs && make html && cd -) - ls -lt docs/_build - pwd - python devtools/ci/push-docs-to-s3.py -fi diff --git a/devtools/travis-ci/index.html b/devtools/travis-ci/index.html deleted file mode 100644 index 576994b0d..000000000 --- a/devtools/travis-ci/index.html +++ /dev/null @@ -1 +0,0 @@ - diff --git a/devtools/travis-ci/install.sh b/devtools/travis-ci/install.sh deleted file mode 100644 index 53193fd37..000000000 --- a/devtools/travis-ci/install.sh +++ /dev/null @@ -1,33 +0,0 @@ -# Temporarily change directory to $HOME to install software -pushd . -cd $HOME - -# Install Miniconda -if [ "$TRAVIS_OS_NAME" == "osx" ]; then - # Make OSX md5 mimic md5sum from linux, alias does not work - md5sum () { - command md5 -r "$@" - } - MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh -else - MINICONDA=Miniconda3-latest-Linux-x86_64.sh - export PYTHON_VER=$TRAVIS_PYTHON_VERSION -fi -MINICONDA_HOME=$HOME/miniconda -MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') -wget -q https://repo.continuum.io/miniconda/$MINICONDA -if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then - echo "Miniconda MD5 mismatch" - exit 1 -fi -bash $MINICONDA -b -p $MINICONDA_HOME - -# Configure miniconda -export PIP_ARGS="-U" -export PATH=$MINICONDA_HOME/bin:$PATH -conda config --add channels conda-forge -conda config --set always_yes yes -conda install conda conda-build jinja2 anaconda-client -conda update --quiet --all - -popd diff --git a/devtools/travis-ci/oe_license.txt.enc b/devtools/travis-ci/oe_license.txt.enc deleted file mode 100644 index 0b27252ea..000000000 Binary files a/devtools/travis-ci/oe_license.txt.enc and /dev/null differ diff --git a/devtools/travis-ci/push-docs-to-s3.py b/devtools/travis-ci/push-docs-to-s3.py deleted file mode 100644 index 7a59350ed..000000000 --- a/devtools/travis-ci/push-docs-to-s3.py +++ /dev/null @@ -1,40 +0,0 @@ -import os -import pip -import tempfile -import subprocess -import thermopyl.version - - -BUCKET_NAME = 'thermopyl.org' -if not thermopyl.version.release: - PREFIX = 'latest' -else: - PREFIX = thermopyl.version.short_version - -if not any(d.project_name == 's3cmd' for d in pip.get_installed_distributions()): - raise ImportError('The s3cmd pacakge is required. try $ pip install s3cmd') -# The secret key is available as a secure environment variable -# on travis-ci to push the build documentation to Amazon S3. -with tempfile.NamedTemporaryFile('w') as f: - f.write('''[default] -access_key = {AWS_ACCESS_KEY_ID} -secret_key = {AWS_SECRET_ACCESS_KEY} -'''.format(**os.environ)) - f.flush() - - template = ('s3cmd --guess-mime-type --config {config} ' - 'sync docs/_build/ s3://{bucket}/{prefix}/') - cmd = template.format( - config=f.name, - bucket=BUCKET_NAME, - prefix=PREFIX) - return_val = subprocess.call(cmd.split()) - - # Sync index file. - template = ('s3cmd --guess-mime-type --config {config} ' - 'sync devtools/ci/index.html s3://{bucket}/') - cmd = template.format( - config=f.name, - bucket=BUCKET_NAME) - return_val = subprocess.call(cmd.split()) - diff --git a/environment.yml b/environment.yml index 14c19c37d..5a6190ca4 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - openeye dependencies: - - python >=3.6 + - python >=3.8 - setuptools - fire - joblib diff --git a/examples/freesolv/mapping-example/README.py b/examples/freesolv/mapping-example/README.md similarity index 100% rename from examples/freesolv/mapping-example/README.py rename to examples/freesolv/mapping-example/README.md diff --git a/perses/annihilation/relative.py b/perses/annihilation/relative.py index be5913557..7a47833e4 100644 --- a/perses/annihilation/relative.py +++ b/perses/annihilation/relative.py @@ -2186,7 +2186,7 @@ def __init__(self, force_names = getattr(self, '_{}_system_forces'.format(system_name)).keys() unknown_forces = set(force_names) - set(self._known_forces) if len(unknown_forces) > 0: - raise ValueError("Unkown forces {} encountered in {} system" % (unknown_forces, system_name)) + raise ValueError(f"Unkown forces {unknown_forces} encountered in {system_name} system") _logger.info("No unknown forces.") # Get and store the nonbonded method from the system: diff --git a/perses/dispersed/smc.py b/perses/dispersed/smc.py index d27f1e84b..0ccf3334c 100644 --- a/perses/dispersed/smc.py +++ b/perses/dispersed/smc.py @@ -515,7 +515,7 @@ def sMC(self, _logger.debug(f"sMC_timers: {sMC_timers}") sMC_incremental_works = {_direction: None for _direction in directions} - _logger.debug(f"\tsMC_incremental_works: {sMC_cumulative_works}") + _logger.debug(f"\tsMC_incremental_works: {sMC_incremental_works}") sMC_cumulative_works = {_direction : [np.zeros(num_particles)] for _direction in directions} @@ -978,7 +978,6 @@ def _resample(self, _logger.debug(f"\t\tnormalized observable value ({normalized_observable_value}) > {resample_observable_threshold}. Skipping resampling.") resampled_works = total_works resampled_indices = np.arange(num_particles) - normalized_observable_value = normalized_observable_value _logger.debug(f"\t\tfinal resampled normalized observable_value: {normalized_observable_value}") return normalized_observable_value, resampled_works, resampled_indices, resample_bool diff --git a/perses/rjmc/topology_proposal.py b/perses/rjmc/topology_proposal.py index 4b987d390..0a1a6a578 100644 --- a/perses/rjmc/topology_proposal.py +++ b/perses/rjmc/topology_proposal.py @@ -1710,7 +1710,7 @@ def _find_adjacent_residue_atoms(self, old_topology, new_topology, mutated_resid old_prev_res = [res for res in old_chain.residues() if res.index == prev_res_index][0] assert new_prev_res.name == old_prev_res.name, f"the new residue left adjacent to mutation res (name {new_prev_res.name}) is not the name of the old residue left adjacent to mutation res (name {old_prev_res.name})" - assert new_next_res.name == new_next_res.name, f"the new residue right adjacent to mutation res (name {new_next_res.name}) is not the name of the old residue right adjacent to mutation res (name {old_next_res.name})" + assert new_next_res.name == old_next_res.name, f"the new residue right adjacent to mutation res (name {new_next_res.name}) is not the name of the old residue right adjacent to mutation res (name {old_next_res.name})" new_next_res_to_old_next_res_map = {new_atom.index : old_atom.index for new_atom, old_atom in zip(new_next_res.atoms(), old_next_res.atoms())} new_prev_res_to_old_prev_res_map = {new_atom.index : old_atom.index for new_atom, old_atom in zip(new_prev_res.atoms(), old_prev_res.atoms())}