Merge pull request #249 from glotzerlab/remove-deprecated-features

Remove deprecated features.

.github/ISSUE_TEMPLATE/release.md

@@ -10,9 +10,7 @@ assignees: 'joaander'
 Release checklist:
 
 - [ ] Run *bumpversion*.
-- [ ] Update change log.
-  - ``git log --format=oneline --first-parent `git log -n 1 --pretty=format:%H -- CHANGELOG.rst`...``
-  - [milestone](https://github.com/glotzerlab/gsd/milestones)
+- [ ] Review the change log.
 - [ ] Check for new or duplicate contributors since the last release:
   `comm -13 <(git log LAST_TAG --format="%aN <%aE>" | sort | uniq) <(git log --format="%aN <%aE>" | sort | uniq)`.
   Add entries to `.mailmap` to remove duplicates.

.github/PULL_REQUEST_TEMPLATE.md

@@ -21,15 +21,9 @@ Resolves #???
 <!--- Please build the sphinx documentation and check that any changes to
       documentation display properly. -->
 
-## Change log
-
-<!-- Propose a change log entry. -->
-```
-
-```
-
 ## Checklist:
 
 - [ ] I have reviewed the [**Contributor Guidelines**](https://github.com/glotzerlab/gsd/blob/trunk-patch/CONTRIBUTING.rst).
 - [ ] I agree with the terms of the [**GSD Contributor Agreement**](https://github.com/glotzerlab/gsd/blob/trunk-patch/ContributorAgreement.md).
 - [ ] My name is on the list of contributors (`doc/credits.rst`) in the pull request source branch.
+- [ ] I have added a change log entry to ``CHANGELOG.rst``.

CHANGELOG.rst

@@ -36,7 +36,14 @@ Change Log
 
 *Removed:*
 
-* ``gsd.__version__``.
+* ``gsd.__version__`` - use `gsd.version.version`.
+* ``gsd.hoomd.Snapshot`` - use `gsd.hoomd.Frame`
+  (`#249 <https://github.com/glotzerlab/gsd/pull/249>`__).
+* ``gsd.hoomd.HOOMDTrajectory.read_frame`` - use `gsd.hoomd.HOOMDTrajectory.__getitem__`
+  (`#249 <https://github.com/glotzerlab/gsd/pull/249>`__).
+* The file modes ``'wb'``, ``'wb+'``, ``'rb'``,  ``'rb+'``, ``'ab'``, ``'xb'``, and ``'xb+'``. Use
+  ``'r'``, ``'r+'``, ``'w'``, ``'x'``, or ``'a'``
+  (`#249 <https://github.com/glotzerlab/gsd/pull/249>`__).
 
 v2.x
 ----

README.md

@@ -40,7 +40,7 @@ Append frames to a gsd file:
 ...     s.particles.N = 4+i;
 ...     s.particles.position = numpy.random.random(size=(4+i,3))
 ...     return s;
->>> with gsd.hoomd.open('test.gsd', 'ab') as t:
+>>> with gsd.hoomd.open('test.gsd', 'a') as t:
 ...     t.extend( (create_frame(i) for i in range(10)) )
 ...     print(len(t))
 11

doc/hoomd-examples.rst

@@ -68,9 +68,6 @@ Write frames to a gsd file
 `append <gsd.hoomd.HOOMDTrajectory.append>` and `extend <gsd.hoomd.HOOMDTrajectory.extend>` methods
 add frames to the trajectory.
 
-.. note:: `gsd.hoomd.HOOMDTrajectory` currently does not support files opened in
-          the 'ab' mode.
-
 .. tip:: When using `extend <gsd.hoomd.HOOMDTrajectory.extend>`, pass in a
          generator or generator expression to avoid storing the entire
          trajectory in memory before writing it out.

gsd/fl.pyx

@@ -195,28 +195,6 @@ def open(name, mode, application=None, schema=None, schema_version=None):
     When opening a file for writing (``'w'``, ``'x'``, or ``'a'`` modes): The
     given ``application``, ``schema``, and ``schema_version`` must not be None.
 
-    .. deprecated:: 2.9.0
-
-        The following values to ``mode`` are deprecated:
-
-        +------------------+---------------------------------------------+
-        | mode             | description                                 |
-        +==================+=============================================+
-        | ``'rb'``         | Equivalent to ``'r'``                       |
-        +------------------+---------------------------------------------+
-        | ``'rb+'``        | Equivalent to ``'r+'``                      |
-        +------------------+---------------------------------------------+
-        | ``'wb'``         | Equivalent to ``'w'``                       |
-        +------------------+---------------------------------------------+
-        | ``'wb+'``        | Equivalent to ``'w'``                       |
-        +------------------+---------------------------------------------+
-        | ``'xb'``         | Equivalent to ``'x'``                       |
-        +------------------+---------------------------------------------+
-        | ``'xb+'``        | Equivalent to ``'x'``                       |
-        +------------------+---------------------------------------------+
-        | ``'ab'``         | Equivalent to ``'r+'``                      |
-        +------------------+---------------------------------------------+
-
     Example:
 
         .. ipython:: python
@@ -317,35 +295,6 @@ cdef class GSDFile:
 
         self.mode = mode
 
-        if mode == 'wb':
-            mode = 'w'
-            warnings.warn("The 'wb' mode is deprecated, use 'w'",
-                           FutureWarning)
-        elif mode == 'wb+':
-            mode = 'w'
-            warnings.warn("The 'wb+' mode is deprecated, use 'w'",
-                           FutureWarning)
-        elif mode == 'rb':
-            mode = 'r'
-            warnings.warn("The 'rb' mode is deprecated, use 'r'",
-                           FutureWarning)
-        elif mode == 'rb+':
-            mode = 'r+'
-            warnings.warn("The 'rb+' mode is deprecated, use 'r+'",
-                           FutureWarning)
-        elif mode == 'xb':
-            mode = 'x'
-            warnings.warn("The 'xb' mode is deprecated, use 'x'",
-                           FutureWarning)
-        elif mode == 'xb+':
-            mode = 'x'
-            warnings.warn("The 'xb+' mode is deprecated, use 'x'",
-                           FutureWarning)
-        elif mode == 'ab':
-            mode = 'r+'
-            warnings.warn("The 'ab' mode is deprecated, use 'r+'",
-                           FutureWarning)
-
         if mode == 'w':
             c_flags = libgsd.GSD_OPEN_READWRITE
             overwrite = 1

gsd/hoomd.py

@@ -407,18 +407,33 @@ def validate(self):
             self.group = self.group.reshape([self.N, self.M])
 
 
-class Snapshot(object):
+class Frame:
     """System state at one point in time.
 
-    .. deprecated:: 2.8.0
+    Attributes:
+        configuration (`ConfigurationData`): Configuration data.
+
+        particles (`ParticleData`): Particles.
+
+        bonds (`BondData`): Bonds.
+
+        angles (`BondData`): Angles.
+
+        dihedrals (`BondData`): Dihedrals.
+
+        impropers (`BondData`): Impropers.
+
+        pairs (`BondData`): Special pair.
 
-        Replaced by `Frame`.
+        constraints (`ConstraintData`): Distance constraints.
+
+        state (dict): State data.
+
+        log (dict): Logged data (values must be `numpy.ndarray` or
+            `array_like`)
     """
 
     def __init__(self):
-        if not isinstance(self, Frame):
-            warnings.warn("Snapshot is deprecated, use Frame", FutureWarning)
-
         self.configuration = ConfigurationData()
         self.particles = ParticleData()
         self.bonds = BondData(2)
@@ -617,36 +632,6 @@ def validate(self):
                 raise RuntimeError('Not a valid state: ' + k)
 
 
-class Frame(Snapshot):
-    """System state at one point in time.
-
-    Attributes:
-        configuration (`ConfigurationData`): Configuration data.
-
-        particles (`ParticleData`): Particles.
-
-        bonds (`BondData`): Bonds.
-
-        angles (`BondData`): Angles.
-
-        dihedrals (`BondData`): Dihedrals.
-
-        impropers (`BondData`): Impropers.
-
-        pairs (`BondData`): Special pair.
-
-        constraints (`ConstraintData`): Distance constraints.
-
-        state (dict): State data.
-
-        log (dict): Logged data (values must be `numpy.ndarray` or
-            `array_like`)
-    """
-
-    def __init__(self):
-        super().__init__()
-
-
 class _HOOMDTrajectoryIterable(object):
     """Iterable over a HOOMDTrajectory object."""
 
@@ -858,7 +843,7 @@ def extend(self, iterable):
         for item in iterable:
             self.append(item)
 
-    def read_frame(self, idx):
+    def _read_frame(self, idx):
         """Read the frame at the given index from the file.
 
         Args:
@@ -871,14 +856,7 @@ def read_frame(self, idx):
         from frame 0, or initialize from default values if not in frame 0. Cache
         frame 0 data to avoid file read overhead. Return any default data as
         non-writable numpy arrays.
-
-        .. deprecated:: v2.5
         """
-        warnings.warn("Deprecated, trajectory[idx]", FutureWarning)
-        return self._read_frame(idx)
-
-    def _read_frame(self, idx):
-        """Implements read_frame."""
         if idx >= len(self):
             raise IndexError
 
@@ -1095,27 +1073,6 @@ def open(name, mode='r'):
     |                  | Creates the file if it doesn't exist.       |
     +------------------+---------------------------------------------+
 
-    .. deprecated:: 2.9.0
-
-        The following values to ``mode`` are deprecated:
-
-        +------------------+---------------------------------------------+
-        | mode             | description                                 |
-        +==================+=============================================+
-        | ``'rb'``         | Equivalent to ``'r'``                       |
-        +------------------+---------------------------------------------+
-        | ``'rb+'``        | Equivalent to ``'r+'``                      |
-        +------------------+---------------------------------------------+
-        | ``'wb'``         | Equivalent to ``'w'``                       |
-        +------------------+---------------------------------------------+
-        | ``'wb+'``        | Equivalent to ``'w'``                       |
-        +------------------+---------------------------------------------+
-        | ``'xb'``         | Equivalent to ``'x'``                       |
-        +------------------+---------------------------------------------+
-        | ``'xb+'``        | Equivalent to ``'x'``                       |
-        +------------------+---------------------------------------------+
-        | ``'ab'``         | Equivalent to ``'r+'``                      |
-        +------------------+---------------------------------------------+
     """
     if fl is None:
         raise RuntimeError("file layer module is not available")

gsd/test/test_fl.py

@@ -978,7 +978,7 @@ def test_flush(tmp_path, open_mode, n_flush):
         # Ensure that the data is buffered by opening the file with a 2nd
         # handle read-only and checking it.
         with gsd.fl.open(name=tmp_path / 'test_flush.gsd',
-                         mode='rb') as f_readonly:
+                         mode='r') as f_readonly:
             assert not f_readonly.chunk_exists(frame=0, name='chunk1')
             assert not f_readonly.chunk_exists(frame=1, name='chunk2')
             assert f_readonly.nframes == 0