Merge pull request #1703 from dib-lab/v2.1/final-tweaks

[MRG] Minor tweaks

author-skips.txt

@@ -1,7 +1,11 @@
 root
+# Duplicates
 [email protected]
 [email protected]
+Sydney Pickens
+# First author
 standage
+# Last author
 titus
 waffleio
 Hello

authors.csv

@@ -60,7 +60,6 @@ Scott Sievert,[email protected]
 Shannon EK Joslin,[email protected]
 Sherine Awad,[email protected]
 Susan R Steinman,[email protected]
-Sydney Pickens,[email protected]
 Tamer Mansour,[email protected]
 Thomas Fenzl,[email protected]
 Tim Head,[email protected]

doc/index.rst

@@ -87,10 +87,10 @@ Details
         McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R.
         Nahum, Kaben Nanlohy, Russell Neches, Alexander Johan Nederbragt,
         Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney,
-        Sydney Pickens, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah
-        Seaman, Ryan Shean, Scott Sievert, Jared Simpson, Connor T. Skennerton,
-        James Spencer, Ramakrishnan Srinivasan, James A. Stapleton, Joe Stein,
-        Sascha Steinbiss, Susan R Steinman, Cait Sydney, Benjamin Taylor, Will
+        Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Ryan
+        Shean, Scott Sievert, Jared Simpson, Connor T. Skennerton, James
+        Spencer, Ramakrishnan Srinivasan, James A. Stapleton, Joe Stein, Sascha
+        Steinbiss, Susan R Steinman, Cait Sydney, Benjamin Taylor, Will
         Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng
         Zhang, en zyme, C. Titus Brown
 

doc/release-notes/release-2.1.md

@@ -0,0 +1,47 @@
+# khmer v2.0 release notes
+
+We are pleased to announce release version 2.1 of khmer!
+This release includes several new features, bug fixes, and internal changes.
+[CHANGELOG.md](https://github.com/dib-lab/khmer/blob/v2.1/CHANGELOG.md) includes a complete description of changes made since the previous release.
+A concise summary of the most relevant changes is provided below.
+
+The latest version of the khmer documentation is available at https://khmer.readthedocs.org/en/v2.1/.
+
+
+## Items of note
+
+### New features
+
+- New storage class using half a byte per entry. Exposed as SmallCounttable and SmallCountgraph.
+- New Counttable, SmallCounttable, and Nodetable classes to support non-reversible hashing functionality and k > 32.
+- Support for human-friendly memory requests (2G) in addition to the previous style of requests (2000000000 or 2e9).
+- Support for variable-coverage trimming in the `filter-abund-single.py` script.
+- khmer package version now included in `.info` files.
+- Several simple examples of the Python API and the C++ API in `examples/python-api` and `examples/c++-api`, respectively.
+- Support for assembling directly from k-mer graphs, and a new JunctionCountAssembler class.
+- New sandbox script `extract-compact-dbg.py` for computing a compact de Bruijn graph from sequence data.
+
+### Bug fixes
+
+- Streaming gzip-compressed output from scripts now works correctly.
+- The `load-graph.py` script now calculates required graph space correctly.
+- The `broken_paired_reader` no longer drops short reads when `require_paired` is set.
+
+### Other changes
+
+- Command-line options `-x` and `-N` now suppressed by default in script help messages.
+- Renamed core data structures: CountingHash --> Countgraph, Hashbits --> Nodegraph.
+- Replaced the `IParser` and `FastxParser` classes with a single `ReadParser` class. Different input formats are supported by templating `ReadParser` with a reader class.
+- Renamed `consume_fasta` and related functions to `consume_seqfile`, with support for reading sequences from additional formats pending.
+
+
+## Known issues:
+
+- `load-graph.py` in multithreaded mode will find slightly different number of unique kmers. This is being investigated in https://github.com/dib-lab/khmer/issues/1248
+- Any scripts that consume FASTA or FASTQ data are unresponsive to attempts to terminate the program with `ctrl-c`. Eventually khmer should handle this properly, but for now it should be possible to halt a script using `ctrl-\`. This is being tracked in https://github.com/dib-lab/khmer/issues/1618.
+
+## Contributors
+
+\*@aaliyari, @ctb, \*@caitsydney, @camillescott, @standage, @kdmurray91, @ljcohen, @luizirber, @mr-c, \*@NBKingsley, \*@ryneches, \*@rcs333, \*@satta, \*@shannonekj, \*@betatim
+
+\* Indicates new contributors

doc/release-notes/release-2.1.rst

@@ -0,0 +1,78 @@
+khmer v2.0 release notes
+========================
+
+We are pleased to announce release version 2.1 of khmer! This release
+includes several new features, bug fixes, and internal changes.
+`CHANGELOG.md <https://github.com/dib-lab/khmer/blob/v2.1/CHANGELOG.md>`__
+includes a complete description of changes made since the previous
+release. A concise summary of the most relevant changes is provided
+below.
+
+The latest version of the khmer documentation is available at
+https://khmer.readthedocs.org/en/v2.1/.
+
+Items of note
+-------------
+
+New features
+~~~~~~~~~~~~
+
+-  New storage class using half a byte per entry. Exposed as
+   SmallCounttable and SmallCountgraph.
+-  New Counttable, SmallCounttable, and Nodetable classes to support
+   non-reversible hashing functionality and k > 32.
+-  Support for human-friendly memory requests (2G) in addition to the
+   previous style of requests (2000000000 or 2e9).
+-  Support for variable-coverage trimming in the
+   ``filter-abund-single.py`` script.
+-  khmer package version now included in ``.info`` files.
+-  Several simple examples of the Python API and the C++ API in
+   ``examples/python-api`` and ``examples/c++-api``, respectively.
+-  Support for assembling directly from k-mer graphs, and a new
+   JunctionCountAssembler class.
+-  New sandbox script ``extract-compact-dbg.py`` for computing a compact
+   de Bruijn graph from sequence data.
+
+Bug fixes
+~~~~~~~~~
+
+-  Streaming gzip-compressed output from scripts now works correctly.
+-  The ``load-graph.py`` script now calculates required graph space
+   correctly.
+-  The ``broken_paired_reader`` no longer drops short reads when
+   ``require_paired`` is set.
+
+Other changes
+~~~~~~~~~~~~~
+
+-  Command-line options ``-x`` and ``-N`` now suppressed by default in
+   script help messages.
+-  Renamed core data structures: CountingHash --> Countgraph, Hashbits
+   --> Nodegraph.
+-  Replaced the ``IParser`` and ``FastxParser`` classes with a single
+   ``ReadParser`` class. Different input formats are supported by
+   templating ``ReadParser`` with a reader class.
+-  Renamed ``consume_fasta`` and related functions to
+   ``consume_seqfile``, with support for reading sequences from
+   additional formats pending.
+
+Known issues:
+-------------
+
+-  ``load-graph.py`` in multithreaded mode will find slightly different
+   number of unique kmers. This is being investigated in
+   https://github.com/dib-lab/khmer/issues/1248
+-  Any scripts that consume FASTA or FASTQ data are unresponsive to
+   attempts to terminate the program with ``ctrl-c``. Eventually khmer
+   should handle this properly, but for now it should be possible to
+   halt a script using ``ctrl-\``. This is being tracked in
+   https://github.com/dib-lab/khmer/issues/1618.
+
+Contributors
+------------
+
+\*@aaliyari, @ctb, \*@caitsydney, @camillescott, @standage, @kdmurray91,
+@ljcohen, @luizirber, @mr-c, \*@NBKingsley, \*@ryneches, \*@rcs333,
+\*@satta, \*@shannonekj, \*@betatim
+
+\* Indicates new contributors