Merge branch 'develop' into double_water

MDAnalysis · May 7, 2021 · aaaec28 · aaaec28
2 parents f60fd9c + da46e84
commit aaaec28
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diff --git a/.disabled-travis.yml b/.disabled-travis.yml
@@ -30,7 +30,7 @@ env:
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
     - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py==2.10.0"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py openmm"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"
@@ -43,7 +43,7 @@ env:
   matrix:
     # Run a coverage test for most versions
     - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-    - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" 
     - PYTHON_VERSION=3.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - NUMPY_VERSION=1.16.0
     - NUMPY_VERSION=dev  EVENT_TYPE="cron"

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -1,4 +1,4 @@
-name: mda_gh_ci
+name: GH Actions CI
 on:
   push:
     branches:
@@ -14,8 +14,8 @@ defaults:
     shell: bash -l {0}
 
 env:
-  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-  MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py==2.10.0"
+  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov threadpoolctl openmm"
+  MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py"
   MDA_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
   MDA_PIP_EXTRA_DEPS: 'duecredit parmed'
 
@@ -28,17 +28,23 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu-latest, ]
-          python-version: [3.6, 3.7, 3.8]
+          python-version: [3.6, 3.7, 3.8, 3.9]
           run_type: [FULL, ]
           install_hole: [true, ]
           codecov: [true, ]
           include:
-            - name: macOS
+            - name: macOS_py39
               os: macOS-latest
-              python-version: 3.7
+              python-version: 3.9
               run_type: FULL
               install_hole: true
               codecov: true
+            - name: macOS_py36_min
+              os: macOS-latest
+              python-version: 3.6
+              run_type: MIN
+              install_hole: false
+              codecov: false
             - name: minimal-ubuntu
               os: ubuntu-latest
               python-version: 3.6
@@ -80,6 +86,7 @@ jobs:
         echo "CXX=clang++" >> $GITHUB_ENV
         gfortran-9 -v
         echo "FC=gfortran-9" >> $GITHUB_ENV
+        echo "numprocs=3" >> $GITHUB_ENV
 
     - name: setup_linux
       if: startsWith(matrix.os, 'ubuntu')
@@ -92,17 +99,17 @@ jobs:
         echo "CXX=g++" >> $GITHUB_ENV
         gfortran -v
         echo "FC=gfortran" >> $GITHUB_ENV
+        echo "numprocs=2" >> $GITHUB_ENV
 
     - name: setup_miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
         auto-update-conda: true
         channel-priority: flexible
-        channels: biobuilds, conda-forge
+        channels: conda-forge, biobuilds
         add-pip-as-python-dependency: true
-        # TODO: mamba causes pip to segfault, switch when fixed
-        #mamba-version: "*"
+        mamba-version: "*"
         architecture: x64
 
     - name: install_deps
@@ -114,7 +121,7 @@ jobs:
         # NOTE: set matrix.numpy to pin to a specific numpy version
         conda_deps="${{ matrix.numpy }} ${MDA_CONDA_${{ matrix.run_type }}_DEPS}"
         pip_deps=${MDA_PIP_${{ matrix.run_type }}_DEPS}
-        conda install ${conda_deps}
+        mamba install ${conda_deps}
         pip install ${pip_deps}
 
         # also install asv if required
@@ -158,7 +165,7 @@ jobs:
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov=MDAnalysis --cov-report=xml"
         fi
         echo $PYTEST_FLAGS
-        pytest -n 2 testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n $numprocs testsuite/MDAnalysisTests $PYTEST_FLAGS
 
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
@@ -191,15 +198,16 @@ jobs:
         python-version: 3.7
         auto-update-conda: true
         channel-priority: flexible
-        channels: biobuilds, conda-forge
+        channels: conda-forge, biobuilds
         add-pip-as-python-dependency: true
         architecture: x64
+        mamba-version: "*"
 
     - name: install_deps
       run: |
         conda_deps="${{ env.MDA_CONDA_MIN_DEPS }} ${{ env.MDA_CONDA_EXTRA_DEPS}}"
         pip_deps="${{ env.MDA_PIP_MIN_DEPS}} ${{ env.MDA_PIP_EXTRA_DEPS }} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0"
-        conda install ${conda_deps}
+        mamba install ${conda_deps}
         pip install ${pip_deps}
 
     - name: install_mda
@@ -280,7 +288,6 @@ jobs:
         channel-priority: flexible
         channels: conda-forge
         add-pip-as-python-dependency: true
-        mamba-version: "*"
         architecture: x64
 
     - name: install
@@ -311,7 +318,7 @@ jobs:
         channel-priority: flexible
         channels: conda-forge
         add-pip-as-python-dependency: true
-        mamba-version: "*"
+        # mamba not enabled as install longer than deps install
         architecture: x64
 
     - name: install_conda

diff --git a/.gitignore b/.gitignore
@@ -39,6 +39,8 @@ authors.py
 *.DS_Store
 # ignore files from tests
 .hypothesis/
+# ignore results from asv
+benchmarks/results
 
 # duecredit
 .duecredit.p

diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,60 @@
+version: ~> 1.0
+language: generic
+group: travis_latest
+
+# Only build for develop
+branches:
+  only:
+    - develop
+
+matrix:
+  fast_finish: true
+  include:
+    - python: 3.8
+      name: "Power PC"
+      os: linux
+      arch: ppc64le
+      if: type = cron
+      before_install:
+        - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh
+        - mkdir $HOME/.conda
+        - bash miniconda.sh -b -p $HOME/miniconda
+        - $HOME/miniconda/bin/conda init bash
+        # for some reason the image does not like sourcing .bashrc
+        - . "/home/travis/miniconda/etc/profile.d/conda.sh"
+        - conda activate base
+        - conda update --yes conda
+        - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base "scipy>=1.6" griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds
+        - pip install pytest-xdist threadpoolctl
+        - conda info
+      install:
+        - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install)
+      script:
+        - pytest testsuite/MDAnalysisTests --disable-pytest-warnings -n 2
+      after_sucess:
+        - echo "Override this stage for now"
+
+    - os: linux
+      language: python
+      arch: arm64-graviton2
+      python: 3.8
+      name: "ARM64"
+      dist: focal
+      virt: vm
+      group: edge
+      if: type = cron
+      before_install:
+        - python -m pip install cython numpy scipy
+        - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm threadpoolctl
+      install:
+        - cd package
+        - python setup.py install
+        - cd ../testsuite
+        - python setup.py install
+        - cd ..
+      script:
+        - cd testsuite
+        - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis
+      after_success:
+        - echo "Override this stage for ARM64"
+
diff --git a/README.rst b/README.rst
@@ -2,7 +2,7 @@
   MDAnalysis Repository README
 ================================
 
-|numfocus| |build| |cov| [*]_
+|numfocus| |build| |travis| |cov| [*]_
 
 |docs| |devdocs| |usergroup| |developergroup| |anaconda| |mybinder|
 
@@ -23,6 +23,9 @@ a `tax-deductible donation`_ to help the project pay for developer time, profess
 
 This project is bound by a `Code of Conduct`_.
 
+|powered_by_MDA|
+
+If you use MDAnalysis_ in your project consider lettting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.
 
 Example analysis script
 =======================
@@ -144,6 +147,7 @@ For citations of included algorithms and sub-modules please see the references_.
 .. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787
 .. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e
 .. _references: https://docs.mdanalysis.org/documentation_pages/references.html
+.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis
 
 
 .. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
@@ -166,8 +170,12 @@ For citations of included algorithms and sub-modules please see the references_.
    :alt: Powered by NumFOCUS
    :target: https://www.numfocus.org/
 
-.. |build| image:: https://travis-ci.com/MDAnalysis/mdanalysis.svg?branch=develop
-   :alt: Build Status
+.. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg
+   :alt: Github Actions Build Status
+   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml
+
+.. |travis| image:: https://img.shields.io/travis/MDAnalysis/mdanalysis/develop?label=Travis%20CI
+   :alt: Travis CI Build Status
    :target: https://travis-ci.com/MDAnalysis/mdanalysis
 
 .. |cov|   image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg
@@ -181,3 +189,7 @@ For citations of included algorithms and sub-modules please see the references_.
 .. |mybinder| image:: https://mybinder.org/badge.svg
    :alt: My Binder
    :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master
+
+.. |powered_by_MDA| image:: https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=15&logo=data:image/x-icon;base64,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
+   :alt: Powered by MDAnalysis
+   :target: https://www.mdanalysis.org
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -35,6 +35,9 @@ jobs:
         Python38-64bit-full:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x64'
+        Python39-64bit-full:
+          PYTHON_VERSION: '3.9'
+          PYTHON_ARCH: 'x64'
   steps:
   - task: UsePythonVersion@0
     inputs:
@@ -44,7 +47,7 @@ jobs:
   - script: python -m pip install --upgrade pip setuptools wheel
     displayName: 'Install tools'
   - script: >-
-      python -m pip install
+      python -m pip install --only-binary=h5py
       cython
       hypothesis
       matplotlib
@@ -54,11 +57,11 @@ jobs:
       pytest-xdist
       scikit-learn
       scipy
-      h5py==2.10.0
+      h5py
       tqdm
+      threadpoolctl
     displayName: 'Install dependencies'
   # TODO: recent rdkit is not on PyPI
-  # NOTE: h5py pinned because of gh-3019
   - script: >-
       python -m pip install
       biopython

diff --git a/benchmarks/benchmarks/ag_methods.py b/benchmarks/benchmarks/ag_methods.py
@@ -403,3 +403,13 @@ def setup(self, universe_type):
 
     def time_find_fragments(self, universe_type):
         frags = self.u.atoms.fragments
+
+
+class FragmentCaching(FragmentFinding):
+    """Test how quickly we find cached fragments"""
+    def setup(self, universe_type):
+        super(FragmentCaching, self).setup(universe_type)
+        frags = self.u.atoms.fragments  # Priming the cache
+
+    def time_find_cached_fragments(self, universe_type):
+        frags = self.u.atoms.fragments
diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - cython
   - griddataformats
   - gsd
-  - h5py==2.10.0
+  - h5py
   - hypothesis
   - joblib>=0.12
   - matplotlib==3.2.2
@@ -31,4 +31,4 @@ dependencies:
       - duecredit
       - parmed
       - msmb_theme==1.2.0
-      - sphinx-sitemap==1.0.2
+      - sphinx-sitemap==1.0.2
diff --git a/package/AUTHORS b/package/AUTHORS
@@ -154,7 +154,19 @@ Chronological list of authors
   - Karthikeyan Singaravelan
 2021
   - Aditya Kamath
-
+  - Leonardo Barneschi
+  - Henrik Jäger
+  - Jan Stevens
+  - Orion Cohen
+  - Dimitrios Papageorgiou
+  - Hannah Pollak
+  - Estefania Barreto-Ojeda
+  - Paarth Thadani
+  - Henry Kobin
+  - Kosuke Kudo
+  - Sulay Shah
+  - Alexander Yang
+
 External code
 -------------