From 1a8759cfd9931edb895381227d7b0d14d7054890 Mon Sep 17 00:00:00 2001 From: richard Date: Tue, 9 Jun 2020 07:50:20 +0100 Subject: [PATCH 1/8] finalised 1.0.0 changelog renamed 0.21.0 references to 1.0 --- package/CHANGELOG | 4 ++-- package/MDAnalysis/analysis/align.py | 4 ++-- package/MDAnalysis/analysis/gnm.py | 4 +--- .../analysis/hbonds/hbond_analysis.py | 4 +--- .../analysis/hydrogenbonds/hbond_analysis.py | 2 +- package/MDAnalysis/analysis/psa.py | 4 ++-- package/MDAnalysis/coordinates/XDR.py | 2 +- package/MDAnalysis/coordinates/XYZ.py | 2 +- package/MDAnalysis/core/_get_readers.py | 2 +- package/MDAnalysis/core/groups.py | 12 +++++----- package/MDAnalysis/core/topologyattrs.py | 10 ++++----- package/MDAnalysis/core/topologyobjects.py | 6 ++--- package/MDAnalysis/core/universe.py | 22 +++++++++---------- package/MDAnalysis/lib/correlations.py | 2 +- package/MDAnalysis/topology/TOPParser.py | 2 +- package/MDAnalysis/topology/XYZParser.py | 2 +- 16 files changed, 40 insertions(+), 44 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index a7f2b212c03..3929cac03eb 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,14 +13,14 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ -mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira, +06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira, PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96, Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria, ss62171, Luthaf, yuxuanzhuang, abhishandy, mlnance, shfrz, orbeckst, wvandertoorn, cbouy, AmeyaHarmalkar, Oscuro-Phoenix, andrrizzi, WG150, tylerjereddy, Marcello-Sega - * 0.21.0 + * 1.0.0 Fixes * MOL2Writer now accepts both Universes and AtomgGroups (Issue #2717) diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index a7ef3853242..4e6c7f6b197 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -458,7 +458,7 @@ def alignto(mobile, reference, select=None, weights=None, .. _ClustalW: http://www.clustal.org/ .. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/ - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 Added *match_atoms* keyword to toggle atom matching. .. versionchanged:: 0.8 @@ -803,7 +803,7 @@ def __init__(self, mobile, reference=None, select='all', filename=None, already a :class:`MemoryReader` then it is *always* treated as if ``in_memory`` had been set to ``True``. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 .. versionchanged:: 1.0.0 Support for the ``start``, ``stop``, and ``step`` keywords has been diff --git a/package/MDAnalysis/analysis/gnm.py b/package/MDAnalysis/analysis/gnm.py index ab7884124e1..bf1f953f045 100644 --- a/package/MDAnalysis/analysis/gnm.py +++ b/package/MDAnalysis/analysis/gnm.py @@ -395,10 +395,8 @@ class closeContactGNMAnalysis(GNMAnalysis): .. deprecated:: 0.16.0 Instead of ``MassWeight=True`` use ``weights="size"``. - .. versionchanged:: 0.21.0 - MassWeight option (see above deprecation entry). - .. versionchanged:: 1.0.0 + MassWeight option (see above deprecation entry). Changed `selection` keyword to `select` """ diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py index 8b89425c961..e0d34ca721d 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py @@ -383,10 +383,8 @@ class HydrogenBondAnalysis(base.AnalysisBase): DEFAULT_DONORS/ACCEPTORS is now embedded in a dict to switch between default values for different force fields. - .. versionchanged:: 0.21.0 - Added autocorrelation (MDAnalysis.lib.correlations.py) for calculating hydrogen bond lifetime - .. versionchanged:: 1.0.0 + Added autocorrelation (MDAnalysis.lib.correlations.py) for calculating hydrogen bond lifetime ``save_table()`` method has been removed. You can use ``np.save()`` or ``cPickle.dump()`` on :attr:`HydrogenBondAnalysis.table` instead. """ diff --git a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py index 12c48abec27..bab6066b3ac 100644 --- a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py @@ -28,7 +28,7 @@ :Year: 2019 :Copyright: GNU Public License v3 -.. versionadded:: 0.21.0 +.. versionadded:: 1.0.0 This module provides methods to find and analyse hydrogen bonds in a Universe. diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index 011cd34846b..490d8869786 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -1680,7 +1680,7 @@ def plot(self, filename=None, linkage='ward', count_sort=False, dist_matrix_clus clustered distance matrix (reordered) - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 :attr:`tick1On`, :attr:`tick2On`, :attr:`label1On` and :attr:`label2On` changed to :attr:`tick1line`, :attr:`tick2line`, :attr:`label1` and :attr:`label2` due to upstream deprecation (see #2493) @@ -1807,7 +1807,7 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward', \ .. _seaborn: https://seaborn.pydata.org/ - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 :attr:`tick1On`, :attr:`tick2On`, :attr:`label1On` and :attr:`label2On` changed to :attr:`tick1line`, :attr:`tick2line`, :attr:`label1` and :attr:`label2` due to upstream deprecation (see #2493) diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py index 8095323ade9..281f1ff0c71 100644 --- a/package/MDAnalysis/coordinates/XDR.py +++ b/package/MDAnalysis/coordinates/XDR.py @@ -113,7 +113,7 @@ class XDRBaseReader(base.ReaderBase): Reader. However, the next time the trajectory is opened, the offsets will have to be rebuilt again. - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 XDR offsets read from trajectory if offsets file read-in fails """ diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py index 88678e6e64b..b3f7f380304 100644 --- a/package/MDAnalysis/coordinates/XYZ.py +++ b/package/MDAnalysis/coordinates/XYZ.py @@ -109,7 +109,7 @@ class XYZWriter(base.WriterBase): .. _xyzplugin: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html - .. versionchanged: 0.21.0 + .. versionchanged: 1.0.0 Use elements attribute instead of names attribute, if present """ diff --git a/package/MDAnalysis/core/_get_readers.py b/package/MDAnalysis/core/_get_readers.py index 44123b2e700..b217387a218 100644 --- a/package/MDAnalysis/core/_get_readers.py +++ b/package/MDAnalysis/core/_get_readers.py @@ -276,7 +276,7 @@ def get_converter_for(format): If no appropriate parser could be found. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ try: writer = _CONVERTERS[format] diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index f3fb36dfba6..8b0531f9052 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -802,7 +802,7 @@ def center(self, weights, pbc=False, compound='group', unwrap=False): .. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'`` compounds .. versionchanged:: 0.20.0 Added `unwrap` parameter - .. versionchanged:: 0.21.0 Removed flags affecting default behaviour + .. versionchanged:: 1.0.0 Removed flags affecting default behaviour """ atoms = self.atoms @@ -933,7 +933,7 @@ def center_of_geometry(self, pbc=False, compound='group', unwrap=False): .. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'`` compounds .. versionchanged:: 0.20.0 Added `unwrap` parameter - .. versionchanged:: 0.21.0 Removed flags affecting default behaviour + .. versionchanged:: 1.0.0 Removed flags affecting default behaviour """ return self.center(None, pbc=pbc, compound=compound, unwrap=unwrap) @@ -1107,7 +1107,7 @@ def bbox(self, pbc=False): .. versionadded:: 0.7.2 .. versionchanged:: 0.8 Added *pbc* keyword - .. versionchanged:: 0.21.0 Removed flags affecting default behaviour + .. versionchanged:: 1.0.0 Removed flags affecting default behaviour """ atomgroup = self.atoms @@ -3043,7 +3043,7 @@ def ureybradley(self): If the :class:`AtomGroup` is not length 2 - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ if len(self) != 2: raise ValueError( @@ -3061,7 +3061,7 @@ def cmap(self): If the :class:`AtomGroup` is not length 5 - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ if len(self) != 5: raise ValueError( @@ -3104,7 +3104,7 @@ def convert_to(self, package): No converter was found for the required package - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ converter = get_converter_for(package) return converter().convert(self.atoms) diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py index 786643316ae..60ce5e9ad51 100644 --- a/package/MDAnalysis/core/topologyattrs.py +++ b/package/MDAnalysis/core/topologyattrs.py @@ -1931,7 +1931,7 @@ def _check_connection_values(func): - coerces them to tuples of ints (for hashing) - ensures that first value is less than last (reversibility & hashing) - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ @functools.wraps(func) @@ -1955,7 +1955,7 @@ def wrapper(self, values, *args, **kwargs): class _Connection(AtomAttr): """Base class for connectivity between atoms - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 Added type checking to atom index values. """ @@ -2044,7 +2044,7 @@ def _add_bonds(self, values, types=None, guessed=True, order=None): @_check_connection_values def _delete_bonds(self, values): """ - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ to_check = set(values) @@ -2231,7 +2231,7 @@ class UreyBradleys(_Connection): These indices refer to the atom indices. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ attrname = 'ureybradleys' singular = 'ureybradleys' @@ -2272,7 +2272,7 @@ class Impropers(_Connection): class CMaps(_Connection): """ A connection between five atoms - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ attrname = 'cmaps' singular = 'cmaps' diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py index 2dfbd23ac51..1f067f5c754 100644 --- a/package/MDAnalysis/core/topologyobjects.py +++ b/package/MDAnalysis/core/topologyobjects.py @@ -337,7 +337,7 @@ class UreyBradley(TopologyObject): ``!=`` operators. A UreyBradley angle is equal to another if the same atom numbers are involved. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ btype = 'ureybradley' @@ -369,7 +369,7 @@ class CMap(TopologyObject): Coupled-torsion correction map term between five :class:`~MDAnalysis.core.groups.Atom` instances. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ btype = 'cmap' @@ -568,7 +568,7 @@ class TopologyGroup(object): .. versionchanged:: 0.19.0 Empty TopologyGroup now returns correctly shaped empty array via indices property and to_indices() - .. versionchanged::0.21.0 + .. versionchanged::1.0.0 ``type``, ``guessed``, and ``order`` are no longer reshaped to arrays with an extra dimension """ diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py index 160bd6a328b..f0f5a6ca86e 100644 --- a/package/MDAnalysis/core/universe.py +++ b/package/MDAnalysis/core/universe.py @@ -456,7 +456,7 @@ def empty(cls, n_atoms, n_residues=1, n_segments=1, .. versionadded:: 0.17.0 .. versionchanged:: 0.19.0 The attached Reader when trajectory=True is now a MemoryReader - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 Universes can now be created with 0 atoms """ if not n_atoms: @@ -981,7 +981,7 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False, None, or an iterable of hashable values with the same length as ``values`` - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ if all(isinstance(x, TopologyObject) for x in values): try: @@ -1061,7 +1061,7 @@ def add_bonds(self, values, types=None, guessed=False, order=None): u2.add_bonds(u.bonds.to_indices()) - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._add_topology_objects('bonds', values, types=types, guessed=guessed, order=order) @@ -1083,7 +1083,7 @@ def add_angles(self, values, types=None, guessed=False): guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._add_topology_objects('angles', values, types=types, guessed=guessed) @@ -1105,7 +1105,7 @@ def add_dihedrals(self, values, types=None, guessed=False): bool, or an iterable of hashable values with the same length as ``values`` - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._add_topology_objects('dihedrals', values, types=types, guessed=guessed) @@ -1127,7 +1127,7 @@ def add_impropers(self, values, types=None, guessed=False): bool, or an iterable of hashable values with the same length as ``values`` - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._add_topology_objects('impropers', values, types=types, guessed=guessed) @@ -1145,7 +1145,7 @@ def _delete_topology_objects(self, object_type, values): If AtomGroups, TopologyObjects, or a TopologyGroup are passed, they *must* be from the same Universe. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ indices = [] for x in values: @@ -1199,7 +1199,7 @@ def delete_bonds(self, values): u.delete_bonds(u2.bonds.to_indices()) - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._delete_topology_objects('bonds', values) self._cache.pop('fragments', None) @@ -1216,7 +1216,7 @@ def delete_angles(self, values): they *must* be from the same Universe. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._delete_topology_objects('angles', values) @@ -1232,7 +1232,7 @@ def delete_dihedrals(self, values): they *must* be from the same Universe. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._delete_topology_objects('dihedrals', values) @@ -1248,7 +1248,7 @@ def delete_impropers(self, values): they *must* be from the same Universe. - .. versionadded:: 0.21.0 + .. versionadded:: 1.0.0 """ self._delete_topology_objects('impropers', values) diff --git a/package/MDAnalysis/lib/correlations.py b/package/MDAnalysis/lib/correlations.py index 483b5fcf97e..494e5482a11 100644 --- a/package/MDAnalysis/lib/correlations.py +++ b/package/MDAnalysis/lib/correlations.py @@ -29,7 +29,7 @@ :Year: 2020 :Copyright: GNU Public License v2 -.. versionadded:: 0.21.0 +.. versionadded:: 1.0.0 This module is primarily for internal use by other analysis modules. It provides functionality for calculating the time autocorrelation function diff --git a/package/MDAnalysis/topology/TOPParser.py b/package/MDAnalysis/topology/TOPParser.py index 53fde99a02a..fe0f0326873 100644 --- a/package/MDAnalysis/topology/TOPParser.py +++ b/package/MDAnalysis/topology/TOPParser.py @@ -157,7 +157,7 @@ class TOPParser(TopologyReaderBase): parses both amber10 and amber12 formats .. versionchanged:: 0.19.0 parses bonds, angles, dihedrals, and impropers - .. versionchanged:: 0.21.0 + .. versionchanged:: 1.0.0 warns users that chamber-style topologies are not current supported """ format = ['TOP', 'PRMTOP', 'PARM7'] diff --git a/package/MDAnalysis/topology/XYZParser.py b/package/MDAnalysis/topology/XYZParser.py index c1167cab275..66f05a5eb2d 100644 --- a/package/MDAnalysis/topology/XYZParser.py +++ b/package/MDAnalysis/topology/XYZParser.py @@ -71,7 +71,7 @@ class XYZParser(TopologyReaderBase): .. versionadded:: 0.9.1 - .. versionchanged: 0.21.0 + .. versionchanged: 1.0.0 Store elements attribute, based on XYZ atom names """ format = 'XYZ' From 85ebe4355c419bf5c477f05ca87318e03af6800c Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 09:05:59 +0100 Subject: [PATCH 2/8] bumped version number to 1.0.0 --- package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index e54eb17bc7c..32ed65f97da 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -67,4 +67,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "0.20.2-dev0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "1.0.0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index 39a13a95a10..12aeec3a958 100755 --- a/package/setup.py +++ b/package/setup.py @@ -73,7 +73,7 @@ from commands import getoutput # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "0.20.2-dev0" +RELEASE = "1.0.0" is_release = 'dev' not in RELEASE diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 76beb028467..d7f07dfd441 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -98,7 +98,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "0.20.2-dev0" +__version__ = "1.0.0" # Do NOT import MDAnalysis at this level. Tests should do it themselves. diff --git a/testsuite/setup.py b/testsuite/setup.py index 52cfef47471..3b0ef20806e 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -88,7 +88,7 @@ def run(self): if __name__ == '__main__': # this must be in-sync with MDAnalysis - RELEASE = "0.20.2-dev0" + RELEASE = "1.0.0" with open("README") as summary: LONG_DESCRIPTION = summary.read() From 1a9e1956c656bb9966871310f9c94108e5d9c038 Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 10:08:41 +0100 Subject: [PATCH 3/8] bumped version to 1.0.1 --- package/CHANGELOG | 10 ++++++++++ package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 5 files changed, 14 insertions(+), 4 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 3929cac03eb..5482a489c99 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,6 +13,16 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ +??/??/?? richardjgowers + + * 1.0.1 + +Fixes + +Enhancements + + + 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira, PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96, Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria, diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index 32ed65f97da..c20e0b44cba 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -67,4 +67,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "1.0.0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "1.0.0-dev0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index 12aeec3a958..cf9a467ba73 100755 --- a/package/setup.py +++ b/package/setup.py @@ -73,7 +73,7 @@ from commands import getoutput # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "1.0.0" +RELEASE = "1.0.1-dev0" is_release = 'dev' not in RELEASE diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index d7f07dfd441..706629937fe 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -98,7 +98,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "1.0.0" +__version__ = "1.0.0-dev0" # Do NOT import MDAnalysis at this level. Tests should do it themselves. diff --git a/testsuite/setup.py b/testsuite/setup.py index 3b0ef20806e..61db8613bd1 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -88,7 +88,7 @@ def run(self): if __name__ == '__main__': # this must be in-sync with MDAnalysis - RELEASE = "1.0.0" + RELEASE = "1.0.0-dev0" with open("README") as summary: LONG_DESCRIPTION = summary.read() From 9dba902d79001a5c7e65cdf76470b21c85a240ba Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 10:10:19 +0100 Subject: [PATCH 4/8] remove python 2.7 from travis CI --- .travis.yml | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/.travis.yml b/.travis.yml index d526eb12d93..75314075761 100644 --- a/.travis.yml +++ b/.travis.yml @@ -65,13 +65,6 @@ matrix: CONDA_DEPENDENCIES="" INSTALL_HOLE="false" - - env: NAME="python 2.7" - PYTHON_VERSION=2.7 - CODECOV="true" - NUMPY_VERSION=1.16 - SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - PIP_DEPENDENCIES="${PIP_DEPENDENCIES} setuptools<45.0.0" - - env: NAME="asv check" PYTHON_VERSION=2.7 CODECOV="false" @@ -85,14 +78,6 @@ matrix: env: PYTHON_VERSION=3.6 NUMPY_VERSION=1.17.3 -# macOS Python 2.7 works in principle but times out on Travis CI: -# Disabled so that the tests can pass. -# - os: osx -# env: PYTHON_VERSION=2.7 -# NUMPY_VERSION=1.16 -# CODECOV="true" -# SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - - env: NAME='minimal' PIP_DEPENDENCIES="" CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES} From c9a17af58a1cd73074b1bb40dda92422e4c3ae6a Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 10:11:40 +0100 Subject: [PATCH 5/8] really increment the version this time --- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 706629937fe..8e1a5db2061 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -98,7 +98,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "1.0.0-dev0" +__version__ = "1.0.1-dev0" # Do NOT import MDAnalysis at this level. Tests should do it themselves. diff --git a/testsuite/setup.py b/testsuite/setup.py index 61db8613bd1..bede9a2551f 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -88,7 +88,7 @@ def run(self): if __name__ == '__main__': # this must be in-sync with MDAnalysis - RELEASE = "1.0.0-dev0" + RELEASE = "1.0.1-dev0" with open("README") as summary: LONG_DESCRIPTION = summary.read() From ec86541e62bb9da8298fd28d9ac76261b39b0997 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Wed, 10 Jun 2020 10:32:18 +0100 Subject: [PATCH 6/8] Update .travis.yml --- .travis.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 75314075761..03a33bf8808 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ env: - GIT_CI_EMAIL=TravisCI@mdanalysis.org - MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html # Set default python version to avoid repetition later - - PYTHON_VERSION=3.5 + - PYTHON_VERSION=3.6 - BUILD_DOCS=false - CODECOV=false - PYTEST_FLAGS="--disable-pytest-warnings --durations=50" @@ -41,7 +41,6 @@ env: - CODECOV="true" SETUP_CMD="${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" - - PYTHON_VERSION=3.6 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - NUMPY_VERSION=1.13.3 - NUMPY_VERSION=dev EVENT_TYPE="cron" From 583f6d0006959c5a35d46fde07da35bde1a37413 Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 10:38:41 +0100 Subject: [PATCH 7/8] derp I'm the best release manager --- package/MDAnalysis/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index c20e0b44cba..7f31bc1218a 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -67,4 +67,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "1.0.0-dev0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "1.0.1-dev0" # NOTE: keep in sync with RELEASE in setup.py From 35a9903f045776ffff5313b4afee42517107bf86 Mon Sep 17 00:00:00 2001 From: richard Date: Wed, 10 Jun 2020 11:11:19 +0100 Subject: [PATCH 8/8] start v2.0 instead 1.0.x will be backports of serious bugs --- package/CHANGELOG | 4 +++- package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 5482a489c99..2cd9bc5a149 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -15,12 +15,14 @@ The rules for this file: ------------------------------------------------------------------------------ ??/??/?? richardjgowers - * 1.0.1 + * 2.0.0 Fixes Enhancements +Deprecations +* Dropped Python 2 support 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira, diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index 7f31bc1218a..0c6a22554ec 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -67,4 +67,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "1.0.1-dev0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "2.0.0-dev0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index cf9a467ba73..371be571dc7 100755 --- a/package/setup.py +++ b/package/setup.py @@ -73,7 +73,7 @@ from commands import getoutput # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "1.0.1-dev0" +RELEASE = "2.0.0-dev0" is_release = 'dev' not in RELEASE diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 8e1a5db2061..e41c7c58083 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -98,7 +98,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "1.0.1-dev0" +__version__ = "2.0.0-dev0" # Do NOT import MDAnalysis at this level. Tests should do it themselves. diff --git a/testsuite/setup.py b/testsuite/setup.py index bede9a2551f..67d3b3d25ca 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -88,7 +88,7 @@ def run(self): if __name__ == '__main__': # this must be in-sync with MDAnalysis - RELEASE = "1.0.1-dev0" + RELEASE = "2.0.0-dev0" with open("README") as summary: LONG_DESCRIPTION = summary.read()