Merge branch 'release/v1.1.1'

.travis.yml

@@ -4,14 +4,14 @@ env:
   - DOC_REMOTE=git@github.com:mordred-descriptor/documentation.git
   - secure: 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
   matrix:
-  - PYTHON_VERSION=3.6 COVERAGE=true DOCUMENTATION=true LINT=true
+  - PYTHON_VERSION=3.6 COVERAGE=true DOCUMENTATION=true
   - PYTHON_VERSION=3.5 COVERAGE=true
   - PYTHON_VERSION=2.7 COVERAGE=true
 os:
 - linux
 - osx
 sudo: false
-before_install: "./extra/ci/before_install.sh"
-install: "./extra/ci/install.sh"
-script: "./extra/ci/test_script.sh"
-after_success: "./extra/ci/after_success.sh"
+before_install: travis_retry ./extra/ci/before_install.sh
+install: travis_retry ./extra/ci/install.sh
+script: travis_retry ./extra/ci/test_script.sh
+after_success: travis_retry ./extra/ci/after_success.sh

Pipfile

@@ -0,0 +1,32 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+networkx = "*"
+six = "*"
+numpy = "*"
+tqdm = "*"
+pandas = "*"
+enum34 = {version = "*", markers="python_version < '3.4'"}
+
+[dev-packages]
+pyyaml = "*"
+nose = "*"
+coverage = "*"
+sphinx = "*"
+sphinx-rtd-theme = "*"
+sphinxcontrib-bibtex = "*"
+coveralls = "*"
+"pep8" = "*"
+isort = "*"
+"flake8" = "*"
+"flake8-quotes" = "*"
+"flake8-print" = "*"
+"flake8-commas" = "*"
+"flake8-comprehensions" = "*"
+"flake8-docstrings" = "*"
+"flake8-sorted-keys" = "*"
+"flake8-regex" = "*"
+"flake8-string-format" = "*"

README.rst

@@ -206,5 +206,5 @@ Documentation
 -  `master <http://mordred-descriptor.github.io/documentation/master>`__
 -  `develop <http://mordred-descriptor.github.io/documentation/develop>`__
 
--  `v1.1.0 <http://mordred-descriptor.github.io/documentation/v1.1.0>`__
+-  `v1.1.0 <http://mordred-descriptor.github.io/documentation/v1.1.1>`__
 -  `v1.0.0 <http://mordred-descriptor.github.io/documentation/v1.0.0>`__

appveyor.yml

@@ -14,9 +14,7 @@ environment:
       MINICONDA: C:\Miniconda35-x64
     - PYTHON_VERSION: 2.7
       MINICONDA: C:\Miniconda-x64
-    - PYTHON_VERSION: 2.7
-      MINICONDA: C:\Miniconda
 
-install: '%CYG_ROOT%/bin/bash ./extra/ci/install.sh'
-test_script: '%CYG_ROOT%/bin/bash ./extra/ci/test_script.sh'
-on_success: '%CYG_ROOT%/bin/bash ./extra/ci/after_success.sh'
+install: appveyor-retry %CYG_ROOT%/bin/bash ./extra/ci/install.sh
+test_script: appveyor-retry %CYG_ROOT%/bin/bash ./extra/ci/test_script.sh
+on_success: appveyor-retry %CYG_ROOT%/bin/bash ./extra/ci/after_success.sh

docs/mordred.rst

@@ -12,8 +12,6 @@ mordred package
 .. autoclass:: mordred.Calculator
     :members:
 
-.. autofunction:: all_descriptors
-
 .. autofunction:: get_descriptors_from_module
 
 .. toctree::

docs/scripts/gen_default_descs.py

@@ -1,5 +1,7 @@
+import sys
 import load_path
-from mordred import Descriptor, descriptors, get_descriptors_from_module
+from mordred import Descriptor, descriptors, get_descriptors_from_module, __version__
+from distutils.version import StrictVersion
 
 load_path.nop()
 
@@ -55,10 +57,11 @@ def to_rst(self, hide_module=False):
 
 
 def get_all_descriptors():
+    v = StrictVersion(__version__)
     for mdl in descriptors.all:
         ds = []
         for Desc in get_descriptors_from_module(mdl):
-            for desc in Desc.preset():
+            for desc in Desc.preset(v):
                 ds.append(desc)
 
         yield ds

extra/ci/after_success.sh

@@ -2,46 +2,50 @@
 
 set -e
 
-if [[ ! -f ~/.ssh/id_rsa ]]; then
-    exit 0
-fi
-
-source ./extra/ci/conda.sh
+source ./extra/ci/common.sh
 
-[[ -n "$COVERAGE" ]] && coveralls
+if [[ -n "$COVERAGE" ]]; then
+    info coveralls
+fi
 
 if [[ -z "$TRAVIS_TAG" && -z "$APPVEYOR_REPO_TAG_NAME" ]]; then
     LABEL=dev
-    echo $(cat mordred/_version.txt).post1.dev1 > mordred/_version.txt
+    python extra/ci/bump-beta-version.py $(cat mordred/_version.txt) > mordred/_version.txt
 else
     LABEL=main
 fi
 
-conda build . --no-test
+info conda build . --no-test
 
 OUTPUT=`conda build . --output --python $PYTHON_VERSION`
-if [[ -n "$APPVEYOR" ]]; then
-    cmd /c "anaconda -t $ANACONDA_CLOUD_TOKEN upload --label $LABEL --force $OUTPUT"
-else
-    anaconda -t $ANACONDA_CLOUD_TOKEN upload --label $LABEL --force $OUTPUT
+if [[ -n "$ANACONDA_CLOUD_TOKEN" ]]; then
+    if [[ -n "$APPVEYOR" ]]; then
+        cmd /c "anaconda -t $ANACONDA_CLOUD_TOKEN upload --label $LABEL --force $OUTPUT"
+    else
+        anaconda -t $ANACONDA_CLOUD_TOKEN upload --label $LABEL --force $OUTPUT
+    fi
 fi
 
 # documentation
-if [[ "$TRAVIS_PULL_REQUEST" == false && -n "$DOCUMENTATION" && "$TRAVIS_OS_NAME" == linux ]]; then
+if [[ -f ~/.ssh/id_rsa && "$TRAVIS_PULL_REQUEST" == false && -n "$DOCUMENTATION" && "$TRAVIS_OS_NAME" == linux ]]; then
     eval $(ssh-agent -s)
     ssh-add
     ssh-add -l
     echo "$SSH_AGENT_PID"
 
     cd docs
-    make html
+    info make html
 
-    git clone -b gh-pages $DOC_REMOTE gh-pages
-    rm -r gh-pages/$TRAVIS_BRANCH || true
-    cp -r _build/html gh-pages/$TRAVIS_BRANCH
+    rm -rf gh-pages
+    info git clone -b gh-pages $DOC_REMOTE gh-pages
+    if [[ -d gh-pages/$TRAVIS_BRANCH ]]; then
+        info rm -r gh-pages/$TRAVIS_BRANCH
+    fi
+    mkdir -p gh-pages/$(dirname $TRAVIS_BRANCH)
+    info cp -r _build/html gh-pages/$TRAVIS_BRANCH
 
     cd gh-pages
-    git add .
-    git commit -m "update documentation to mordred-descriptor/mordred@$TRAVIS_COMMIT"
-    git push origin gh-pages
+    info git add .
+    info git commit -m "update documentation to mordred-descriptor/mordred@$TRAVIS_COMMIT"
+    info git push origin gh-pages
 fi

extra/ci/bump-beta-version.py

@@ -0,0 +1,11 @@
+from distutils.version import StrictVersion
+import sys
+
+
+def main(version):
+    (major, minor, patch) = StrictVersion(version).version
+    print("{}.{}.{}a1".format(major, minor, patch + 1))
+
+
+if __name__ == "__main__":
+    main(sys.argv[1])

extra/ci/conda.sh → extra/ci/common.sh

@@ -5,3 +5,13 @@ if [[ -n "$APPVEYOR" ]]; then
 else
     export PATH="$HOME/miniconda/bin:$PATH"
 fi
+
+info() {
+    echo ">>> $@"
+    "$@"
+}
+
+banner() {
+    line="=================="
+    echo "$line $@ $line"
+}

extra/ci/get-rdkit-version.py

@@ -0,0 +1,16 @@
+def main(data, os, pyver):
+    d = {
+        (os, pyver): ver
+        for os, pyver, ver
+        in (line.strip().split() for line in open(data))
+    }
+
+    print(d[(os, pyver)])
+
+
+if __name__ == "__main__":
+    import sys
+    import os
+
+    data = os.path.join(os.path.dirname(__file__), "rdkit-versions.txt")
+    main(data, *sys.argv[1:])

extra/ci/install.sh

@@ -1,55 +1,49 @@
 #!/bin/bash
-
 set -e
 
-REQUIREMENTS=./extra/requirements
-CONDA_REQ_FILE=requirements-conda.txt
-PIP_REQ_FILE=requirements-pip.txt
+source ./extra/ci/common.sh
 
 # install conda
-
-if [[ "$TRAVIS_OS_NAME" == osx ]]; then
-    export OS_NAME=MacOSX
-elif [[ "$TRAVIS_OS_NAME" == linux ]]; then
-    export OS_NAME=Linux
+if [[ -n "$TRAVIS_OS_NAME" ]]; then
+    if [[ "$TRAVIS_OS_NAME" == osx ]]; then
+        export OS_NAME=MacOSX
+    elif [[ "$TRAVIS_OS_NAME" == linux ]]; then
+        export OS_NAME=Linux
+    fi
+    if [[ ! -f "miniconda.sh" ]]; then
+        info wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-${OS_NAME}-x86_64.sh -O miniconda.sh
+    fi
+    rm -rf $HOME/miniconda
+    info bash miniconda.sh -b -p $HOME/miniconda
 elif [[ -n "$APPVEYOR" ]]; then
     export OS_NAME=Windows
 fi
 
-if [[ -n "$TRAVIS_OS_NAME" ]]; then
-    wget https://repo.continuum.io/miniconda/Miniconda3-latest-${OS_NAME}-x86_64.sh -O miniconda.sh
-    bash miniconda.sh -b -p $HOME/miniconda
-fi
-
-source ./extra/ci/conda.sh
-
 # setup conda
-
 hash -r
 
-conda config --set always_yes yes --set changeps1 no
-conda config --add channels rdkit --add channels mordred-descriptor
+info conda config --set always_yes yes --set changeps1 no
+info conda config --add channels rdkit --add channels mordred-descriptor
+info conda update -y --all
+
+info conda install python=$PYTHON_VERSION
 
 # install requirements
+info pip install pipenv
 
-cat $REQUIREMENTS/requirements-conda.txt $REQUIREMENTS/requirements.txt > $CONDA_REQ_FILE
+pipenv lock -r > requirements.txt
+info python ./extra/ci/scrub-requirements.py requirements.txt
 
-if [[ "$PYTHON_VERSION" < 3.4 ]]; then
-    echo enum34 >> $CONDA_REQ_FILE
-fi
+banner "requirements.txt start"
+cat requirements.txt
+banner "requirements.txt  end "
 
-[[ "$PYTHON_VERSION" < 3.4 ]] && echo enum34 >> $CONDA_REQ_FILE
+RDKIT="rdkit==$(python ./extra/ci/get-rdkit-version.py $OS_NAME $PYTHON_VERSION)"
+info conda install $RDKIT --file requirements.txt --file ./extra/ci/requirements-conda.txt
 
-if [[ -n "$LINT" ]]; then
-    cat $REQUIREMENTS/requirements-flake8.txt >> $PIP_REQ_FILE
-fi
+pipenv lock -r --dev > requirements.txt
+banner "requirements.txt(dev) start"
+cat requirements.txt
+banner "requirements.txt(dev)  end "
 
-if [[ -n "$DOCUMENTATION" ]]; then
-    cat $REQUIREMENTS/requirements-documentation.txt >> $PIP_REQ_FILE
-fi
-
-conda install python=$PYTHON_VERSION --file $CONDA_REQ_FILE
-
-if [[ -f $PIP_REQ_FILE ]]; then
-    pip install -r $PIP_REQ_FILE
-fi
+info pip install -r requirements.txt

extra/ci/rdkit-versions.txt

@@ -0,0 +1,9 @@
+MacOSX  3.6 2018.03.1.0
+MacOSX  3.5 2018.03.1.0
+MacOSX  2.7 2018.03.1.0
+Linux   3.6 2018.03.1.0
+Linux   3.5 2018.03.1.0
+Linux   2.7 2018.03.1.0
+Windows 3.6 2018.03.1.1
+Windows 3.5 2017.09.2.0
+Windows 2.7 2017.09.3.0

extra/requirements/requirements-conda.txt → extra/ci/requirements-conda.txt

@@ -1,3 +1,2 @@
-rdkit>=2015.09.2
 conda-build
 anaconda-client

extra/ci/scrub-requirements.py

@@ -0,0 +1,30 @@
+from __future__ import print_function
+import sys
+import re
+
+
+def main(path):
+    contents = [line.rstrip() for line in open(path)]
+    with open(path, 'w') as dst:
+        for line in contents:
+            if '-' == line[0]:
+                continue
+
+            vs = re.split(r'\s*;\s*', line)
+            if len(vs) == 1:
+                print(line, file=dst)
+                continue
+
+            if len(vs) > 2:
+                raise ValueError("#field > 2")
+
+            v = sys.version_info
+            pkg, cond = vs
+            cond = cond.replace("python_version", '{}.{}'.format(v.major, v.minor))
+            cond = re.sub(r"'(\d+\.\d+)'", r'\1', cond)
+            if eval(cond):
+                print(pkg, file=dst)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1])

extra/ci/test_script.sh

@@ -1,23 +1,25 @@
 #!/bin/bash
 
 set -e
-source ./extra/ci/conda.sh
+source ./extra/ci/common.sh
+
+PYTHON=python
+
+conda list
 
 if [[ -n "$COVERAGE" ]]; then
-    python -m mordred.tests -q --with-coverage
+    info $PYTHON -m mordred.tests -q --with-coverage
 else
-    python -m mordred.tests -q
+    info $PYTHON -m mordred.tests -q
 fi
 
 echo "test README.rst" >&2
-python -m doctest README.rst
+info $PYTHON -m doctest README.rst
 
 for example in `find examples -name '*.py'`; do
     echo "test $example" >&2
-    PYTHONPATH=. python $example > /dev/null
+    PYTHONPATH=. info $PYTHON $example > /dev/null
 done
 
-if [[ -n "$LINT" ]]; then
-    python setup.py flake8
-    python setup.py isort
-fi
+info $PYTHON setup.py flake8
+info $PYTHON setup.py isort