Merge pull request #68 from dwhswenson/release-0.5.0

Release 0.5.0

.gitignore

@@ -3,7 +3,7 @@ dask-worker-space
 *nc
 .pytest_cache
 
-contact_map/version.py
+contact_map/_installed_version.py
 cover
 
 # Byte-compiled / optimized / DLL files

.travis.yml

@@ -1,8 +1,13 @@
+version: ~> 1.0
+
 language: python
 python:
-  - '3.6'
+  - '3.7'
   - '2.7'
-  - '3.5'
+  - '3.6'
+
+notifications:
+  webhooks: https://coveralls.io/webhook
 
 branches:
   only:
@@ -12,7 +17,7 @@ branches:
 
 env:
   global:
-    - CANONICAL_PYTHON="3.6"
+    - CANONICAL_PYTHON="3.7"
     - CANONICAL_MDTRAJ="release"
     - CODECLIMATE=""
     - TWINE_USERNAME="dwhswenson"
@@ -24,13 +29,14 @@ env:
     - MDTRAJ="release"
     - MDTRAJ="dev"
 
-matrix:
+jobs:
   exclude:
     - env: MDTRAJ="dev"
-      python: "3.5"
+      python: "3.6"
 
 before_install:
   - echo "before install"
+  - echo "$TRAVIS_BRANCH $TRAVIS_EVENT_TYPE"
   - git fetch --tags
 
 install:
@@ -44,75 +50,15 @@ install:
 script:
   - export MPLBACKEND=SVG
   - python -c "import contact_map"
-  - python autorelease_check.py --branch ${TRAVIS_BRANCH} --event ${TRAVIS_EVENT_TYPE} --allow-patch-skip  #TODO remove allow-patch-skip
+  - python autorelease_check.py --branch ${TRAVIS_BRANCH} --event ${TRAVIS_EVENT_TYPE} #--allow-patch-skip  # allow-patch-skip if there was a testpypi problem
   - py.test -vv --cov=contact_map --cov-report xml:cov.xml
 
 after_success:
+  - export COVERALLS_PARALLEL=true
   - coveralls
   - python-codacy-coverage -r cov.xml
 
-jobs:
-  include:
-    - stage: deploy testpypi
-      # This stage runs when you make a PR to stable. It tests that the
-      # deployment to testpypi works.
-      if: "(branch = stable) and (type = pull_request)"
-      python: '3.6'
-      addons:
-        apt_packages:
-          - pandoc
-      install:
-        - pip install twine
-      script: 
-        - pandoc --from=markdown --to=rst --output=README.rst README.md
-        - python setup.py sdist bdist_wheel
-        - twine upload --repository-url https://test.pypi.org/legacy/ dist/*
-      after_success: skip
-    - stage: test testpypi
-      # This stage run when you make a PR to stable; after the package has
-      # been deployed to testpypi. It checks that the deployed package
-      # works.
-      if: "(branch = stable) and (type = pull_request)"
-      python: '3.6'
-      install:
-        - source ci/pip-install/install_requirements.sh
-        - pip install -U -r ci/pip-install/testing_requirements.txt
-        - pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple contact_map
-      script:
-        - cd ~
-        - python -c "import contact_map"
-        - py.test --pyargs contact_map
-      after_success: skip
-    - stage: cut release
-      # This stage runs after you merge a PR into stable. It cuts the GitHub
-      # release based on the current stable branch and the release notes
-      # from the last PR merged into stable.
-      if: "(branch = stable) and (not type in (pull_request, cron))"
-      python: '3.6'
-      install:
-        - pip install autorelease
-      script:
-        - VERSION=`python setup.py --version`
-        - PROJECT=`python setup.py --name`
-        - autorelease-release --project $PROJECT --version $VERSION --token $AUTORELEASE_TOKEN
-      after_success: skip
-    - stage: deploy pypi
-      # This stage runs when a version-labelled tag is made. It deploys the
-      # package to PyPI.
-      if: tag =~ ^v[0-9]+\.
-      addons:
-        apt_packages:
-          - pandoc
-      install: skip
-      script:
-          - pandoc --from=markdown --to=rst --output=README.rst README.md
-      after_success: true
-      deploy:
-        provider: pypi
-        distributions: sdist bdist_wheel
-        skip_cleanup: true  # need the readme.rst from the script stage
-        user: dwhswenson
-        on:
-            tags: true
-        password:
-          secure: "UN99BfNgMlE1qOwkbvJYMEdPGVF02dnZ5iF9HZY5HwJr7nlW1ixEGn6SzICS7WwLzthfqpbwXaqVGEsbsn1YwsvQe72JyCZxftoxZC2bVi5JV/OZka5uUTx0NXtzukZp33AUTDA9J2vushIxZCHSJG+GFqx4c+L8Y194V0QS4sw/lbtGC3qZ8jmszCnRgfPbb0tmCe4Jj1snclspPXhYtXL2z9Xh4r+ImCfosBFfThtsUs6t37/Jrx1srmDrt0eaGGBm1NAcyIVP6x03TdVVUFt/ud3U7+o0iHhqdEZKfUc2Dp6YN08Ck6Zyr/dR/A0Sc3/pWvytXwXLzOj+d7BtaAmPApcAc6v5GEmwWc4mkdsD+CEEW1q3CEFbWq6RTL+oa2zvEO6k0VrnHMCni3KqsWGmF6B209tHhy8jFAmCIruD2foUz7NxEKWNEOR4bqIjOGGIgGp4mfH+1l73JrI995ZmB1PqiIkxVeX0nPrZUZtBxOUyxg6aiL+NHMaYr5NCq2uCzDYhtwWnk26Oq6/JAEMxN+SCiC+O+DSvdQaUgUp6eS5whHGvf27ZxRMkmTSYTIMN6V1/PQ9WWSFsy0QBUYB7UJf/JLFnTi5xHj08jFNzUVOmeyq9MBzJF/ztnTTBSJgzNDROV+2qsZC0Ulm/hesMe0Swxqu/S5PelzrgwCA="
+
+import:
+  - dwhswenson/autorelease:[email protected]
+

MANIFEST.in

@@ -1,2 +1,2 @@
-include contact_map/tests/trajectory.pdb
+include contact_map/tests/*.pdb
 include LICENSE

README.md

@@ -8,7 +8,7 @@
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com&utm_medium=referral&utm_content=dwhswenson/contact_map&utm_campaign=Badge_Grade)
 [![Maintainability](https://api.codeclimate.com/v1/badges/84768756d594176d8da6/maintainability)](https://codeclimate.com/github/dwhswenson/contact_map/maintainability)
 
-# Contact Maps
+# Contact Map Explorer
 
 This package provides tools for analyzing and exploring contacts
 (residue-residue and atom-atom) from a trajectory generated by molecular
@@ -20,9 +20,9 @@ processes involving biomolecules. For example, an analysis of contacts can
 be particularly useful when defining bound states during a binding processes
 between proteins, DNA, and small molecules (such as potential drugs).
 
-The contacts analyzed by `contact_map` can be either intermolecular or
-intramolecular, and can be analyzed on a residue-residue basis or an
-atom-atom basis.
+The contacts analyzed by Contact Map Explorer can be either intermolecular or
+intramolecular, and can be analyzed on a residue-residue basis or an atom-atom
+basis.
 
 This package makes it very easy to answer questions like:
 
@@ -59,7 +59,7 @@ for details.
 
 ## Support and development
 
-`contact_map` is an open source project, released under the GNU LGPL,
+Contact Map Explorer is an open source project, released under the GNU LGPL,
 version 2.1 or (at your option) any later version. Development takes place
 in public at https://github.com/dwhswenson/contact_map; your contributions
 would be welcome!

appveyor.yml

@@ -21,24 +21,26 @@ environment:
       CONDA_PY: "27"
       ARCH: '64'
     - PYTHON: "C:\\Miniconda36"
-      CONDA_PY: "36"
+      CONDA_PY: "36" # No MDTraj for py37/Win32
       ARCH: '32'
-    - PYTHON: "C:\\Miniconda36-x64"
-      CONDA_PY: "36"
+    - PYTHON: "C:\\Miniconda37-x64"
+      CONDA_PY: "37"
       ARCH: '64'
 
 build: false
 
 install:
   # install python
   - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
-  # test python version
-  - "%CMD_IN_ENV% conda config --add channels omnia"  # TODO: switch to conda-forge?
-  - "%CMD_IN_ENV% conda update -yq --all"
-  - "%CMD_IN_ENV% conda install -yq \"conda-build<3.0.26\""
-  - "%CMD_IN_ENV% python --version"
-  - "%CMD_IN_ENV% python -c \"import struct; print(struct.calcsize('P') * 8)\""
-  # now we do our own install
+  - conda config --add channels conda-forge
+  - conda install -yq conda=4.5 conda-build=3.10
 
 test_script:
-  - "%CMD_IN_ENV% conda build --quiet ci\\conda-recipe"
+  #- "%CMD_IN_ENV% activate base"
+  #- "%CMD_IN_ENV% python --version"
+  #- "%CMD_IN_ENV% python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  #- "%CMD_IN_ENV% conda build --quiet ci\\conda-recipe"
+  - activate base
+  - python --version
+  - python -c "import struct; print(struct.calcsize('P') * 8)"
+  - conda build --quiet ci\conda-recipe

autorelease_check.py

@@ -3,17 +3,19 @@
 import setup
 import contact_map
 from autorelease import DefaultCheckRunner, conda_recipe_version
+from autorelease.version import get_setup_version
 from packaging.version import Version
 
 repo_path = '.'
+SETUP_VERSION = get_setup_version(None, directory='.')
 versions = {
     'package': contact_map.version.version,
-    'setup.py': setup.PACKAGE_VERSION,
+    'setup.py': SETUP_VERSION,
     'conda-recipe': conda_recipe_version('ci/conda-recipe/meta.yaml'),
 }
 
 RELEASE_BRANCHES = ['stable']
-RELEASE_TAG = "v" + Version(setup.PACKAGE_VERSION).base_version
+RELEASE_TAG = "v" + Version(SETUP_VERSION).base_version
 
 if __name__ == "__main__":
     checker = DefaultCheckRunner(

ci/conda-recipe/meta.yaml

@@ -1,13 +1,12 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.4.0"
+  version: "0.5.0"
 
 source:
   path: ../../
 
 build:
-  preserve_egg_dir: True
   number: 0
   script: python setup.py install --single-version-externally-managed --record record.txt
 
@@ -21,7 +20,7 @@ requirements:
     - mdtraj
     - numpy
     - scipy
-    - pandas
+    - pandas<1.0
 
 test:
   requires:

contact_map/contact_map.py

@@ -61,6 +61,9 @@ def _atom_slice(traj, indices):
     if traj._have_unitcell:
         unitcell_lengths = traj._unitcell_lengths.copy()
         unitcell_angles = traj._unitcell_angles.copy()
+    else:
+        unitcell_lengths = None
+        unitcell_angles = None
     time = traj._time.copy()
 
     # Hackish to make the smart slicing work

contact_map/plot_utils.py

@@ -42,7 +42,7 @@ def ranged_colorbar(cmap, norm, cbmin, cbmax, name="Partial Map"):
     new_norm = matplotlib.colors.Normalize(vmin=cbmin, vmax=cbmax)
     sm = plt.cm.ScalarMappable(cmap=new_cmap, norm=new_norm)
     sm._A = []
-    cb = plt.colorbar(sm)
+    cb = plt.colorbar(sm, fraction=0.046, pad=0.04)
     return cb