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())}
|