[FEATURE] Updates to MDAnalysis v2.0.0 and CI

Merge pull request #58 

* Upgrades to MDAv2.0.0
* Defines version for all other dependencies
* Upgrades CI

.github/workflows/build.yml

@@ -1,5 +1,5 @@
 # this action must be synchronized with version-bump-and-package.yml
-name: test_build
+name: build
 
 on:
   pull_request:
@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: test_docs
+name: docs
 
 on:
   push:

.github/workflows/install-dev.yml

@@ -0,0 +1,42 @@
+name: install-dev
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: taurenmddev
+        environment-file: requirements-dev.yml
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge
+        auto-activate-base: false
+
+    - shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+
+#    - name: Install dependencies
+#      run: |
+#        conda env update -n taurenmddev --file requirements-dev.yml
+
+    - name: Test versions
+      shell: bash -l {0}
+      run: |
+        python -c "from mdtraj import version; print('mdtraj version: ', version.version)"
+        python -c "from openmm import version; print('openmm version: ', version.version)"
+        python -c "from MDAnalysis import version; print('MDAnalysis version: ', version.__version__)"

.github/workflows/install.yml

@@ -0,0 +1,38 @@
+name: install
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: taurenmd
+        environment-file: requirements.yml
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge
+        auto-activate-base: false
+
+    - shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+
+    - name: Test versions
+      shell: bash -l {0}
+      run: |
+        python -c "from mdtraj import version; print('mdtraj version: ', version.version)"
+        python -c "from openmm import version; print('openmm version: ', version.version)"
+        python -c "from MDAnalysis import version; print('MDAnalysis version: ', version.__version__)"

.github/workflows/py36.yml

@@ -1,4 +1,4 @@
-name: test_py36
+name: pytest_py36
 
 on:
   push:

.github/workflows/py37.yml

@@ -1,4 +1,4 @@
-name: test_py37
+name: pytest_py37
 
 on:
   push:

.github/workflows/py38.yml

@@ -0,0 +1,36 @@
+name: pytest_py38
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: test
+        python-version: 3.8
+        channels: conda-forge
+
+    - name: Install dependencies
+      run: |
+        conda install pip setuptools wheel tox coverage[toml]
+
+    - name: Test with tox
+      run: tox -e py38
+
+    # from https://github.com/codecov/codecov-action
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        files: ./coverage.xml
+        fail_ci_if_error: true
+        verbose: true

.github/workflows/py39.yml

@@ -0,0 +1,36 @@
+name: pytest_py39
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: test
+        python-version: 3.9
+        channels: conda-forge
+
+    - name: Install dependencies
+      run: |
+        conda install pip setuptools wheel tox coverage[toml]
+
+    - name: Test with tox
+      run: tox -e py39
+
+    # from https://github.com/codecov/codecov-action
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        files: ./coverage.xml
+        fail_ci_if_error: true
+        verbose: true

CHANGELOG.rst

@@ -10,6 +10,10 @@ Upon version 0.8, and before version 1, SV2 major version increments are reflect
 Changelog
 =========
 
+* Updates MDAnalysis to version 2.0.0
+* Defines versions for all other dependencies
+* Updates CI
+
 v0.9.9 (2021-11-22)
 ------------------------------------------------------------
 

README.rst

@@ -18,7 +18,7 @@ taurenmd
     :alt: Zenodo
 
 .. image:: https://github.com/joaomcteixeira/taurenmd/workflows/Tests/badge.svg?branch=master
-    :target: https://github.com/joaomcteixeira/taurenmd/actions?workflow=test_py37
+    :target: https://github.com/joaomcteixeira/taurenmd/actions?workflow=pytest_py37
     :alt: Test Status
 
 .. image:: https://img.shields.io/readthedocs/taurenmd/latest?label=Read%20the%20Docs

docs/installation.rst

@@ -37,9 +37,10 @@ If you use `Anaconda`_ as your Python package manager just do the following on y
 
 If for some reason the above does not work, just open the link on your WebBrowser and save the text to a file (or save the file).
 
-2. Create a new Anaconda Python environment to host *taurenmd*::
+2. Create a new Anaconda Python environment to host *taurenmd*. Choose the python version that best fits your needs; if you are not sure chose 3.7.::
 
-    conda env create -f taurenmdenv.yml
+    conda create -n taurenmd python=3.8
+    conda env update -n taurenmd --file taurenmddev.yml
 
 Where ``taurenmdenv.yml`` is the file downloaded in the previous step.
 
@@ -87,21 +88,25 @@ We do not provide support for other distribution platforms such as `HomeBrew <ht
 From GitHub
 ```````````
 
-If you are a proficient Pythonista you might want to install **taurenmd** from a development branch on GitHub. If that is the case you might not need to read this section because you already know well what to do; nonetheless, let's go through it:
+If you are a proficient Pythonista you might want to install **taurenmd** directly from the GitHub repository. If that is the case you might not need to read this section because you already know well what to do; nonetheless, let's go through it:
 
 .. note::
 
     ``taurenmd`` follows :ref:`Semantic Version 2.0 <Versioning>`, meaning that every single new addition to the master branch gets released on PyPI with a new version number. Therefore, installing from the ``master`` GitHub branch actually adds no benefit to installing with ``pip``.
 
-#. Install the MD analysis libraries as described in the above sections
 #. Clone our repository: ``git clone https://github.com/joaomcteixeira/taurenmd``
 #. Place yourself in the new ``taurenmd`` folder, in Linux-like systems: ``cd taurenmd``.
-#. ``git checkout -b the-branch-you-want-to-use``
-#. Install **taurenmd** with the following command: ``python setup.py develop``
+#. Install the dependencies using Anaconda. Choose your preferred python version.::
+
+    conda create -n taurenmd python=3.8
+    conda env update -n taurenmd --file requirements-dev.yml
+
+#. Install **taurenmd** with the following command: ``python setup.py develop --no-deps``
 #. In the future, to keep your installation up to the latest:
 
   #. pull repository updates from the upstream repository: ``git pull`` (from within ``taurenmd`` git folder)
-  #. because taurenmd developments are mostly reflected on new interfaces you need to update those as well: ``python setup.py develop``
+  #. because taurenmd developments are mostly reflected on new interfaces you need to update those as well: ``python setup.py develop --no-deps``
+  #. beaware, if the version increment denotes API breaks you might need to reinstall ``taurenmd`` from scratch.
 
 Running taurenmd
 ----------------
@@ -115,9 +120,15 @@ Please read our :ref:`Usage` page for, *whatelse*, usage instructions and exampl
 Upgrade
 -------
 
-To upgrade *taurenmd* and all its dependencies to the latest version::
+To upgrade *taurenmd* and all its dependencies to the latest version:
+
+#. If you installed from PyPI::
+
+    pip3 install -U --force-reinstall taurenmd
+
+#. If you installed from Anaconda::
 
-   pip3 install -U --force-reinstall taurenmd
+    pip3 install -U --force-reinstall taurenmd --no-deps
 
 Something failed
 ----------------

requirements-dev.yml

@@ -4,12 +4,10 @@ channels:
     - omnia
     - defaults
 dependencies:
-    - python=3.7
-    - tox
-    - tox-conda
-    - mdanalysis
-    - mdtraj
-    - openmm
+    - tox=3
+    - mdanalysis=2
+    - mdtraj>=1.9,<2
+    - openmm>=7.6,<8
     - matplotlib=3
     - numpy=1
     - pip

requirements.yml

@@ -4,10 +4,9 @@ channels:
     - omnia
     - defaults
 dependencies:
-    - python=3.7
-    - mdanalysis
-    - mdtraj
-    - openmm
+    - mdanalysis=2
+    - mdtraj>=1.9,<2
+    - openmm>=7.6,<8
     - matplotlib=3
     - numpy=1
     - pip

setup.py

@@ -43,8 +43,8 @@
 
 # Molecular Dynamics deps
 mddeps = [
-    'MDAnalysis>=0.2,<1',
-    'mdtraj>=1,<2',
+    'MDAnalysis==2',
+    'mdtraj>=1.9,<2',
     ]
 
 alldeps = mddeps + supdeps
@@ -91,6 +91,8 @@ def _read(*names, **kwargs):
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
         'Topic :: Utilities',
         ],
     project_urls={
@@ -107,7 +109,7 @@ def _read(*names, **kwargs):
         'Molecular Biology',
         'Biochemistry',
         ],
-    python_requires='>=3.6, <3.8',
+    python_requires='>=3.6, <3.10',
     install_requires=install_requires,
     extras_require={
         'all': alldeps,

src/taurenmd/cli_trajedit.py

@@ -154,7 +154,7 @@ def main(
         traj_output='traj_out.dcd',
         top_output=None,
         unwrap=False,
-        unwrap_reference=None,
+        unwrap_reference='com',
         unwrap_compound='fragments',
         align=False,
         **kwargs,
@@ -165,7 +165,12 @@ def main(
     topology = Path(topology)
     trajectories = [Path(t) for t in trajectories]
 
-    u = libmda.load_universe(topology, *trajectories, insort=insort)
+    u = libmda.load_universe(
+        topology,
+        *trajectories,
+        insort=insort,
+        guess_bonds=unwrap,
+        )
 
     if unwrap:
         log.info(T('unwrapping'))

src/taurenmd/libs/libmda.py

@@ -22,7 +22,11 @@
 
 
 @libcli.add_reference(tcore.ref_mda)
-def load_universe(topology, *trajectories, insort=False):
+def load_universe(
+        topology,
+        *trajectories,
+        insort=False,
+        **universe_args):
     """
     Load MDAnalysis universe.
 
@@ -54,6 +58,13 @@ def load_universe(topology, *trajectories, insort=False):
         Paths to trajectory file(s). Trajectory files will be used
         sequentially to create the Universe.
 
+    insort : bool
+        Whether to sort trajectory files by suffix number.
+        See :func:`libio.sort_numbered_input`.
+
+    universe_args : any
+        Other arguments to be passed to `MDAnalysis Universe`.
+
     Return
     ------
     MDAnalysis Universe
@@ -65,6 +76,7 @@ def load_universe(topology, *trajectories, insort=False):
     universe = mda.Universe(
         Path(topology).str(),
         [Path(i).str() for i in trajectories],
+        **universe_args,
         )
     report(universe)
     return universe