Pre-release cosmetics

CHANGES.md

@@ -1,45 +1,32 @@
-### 0.4.0 (2022-06-XX) ###
+### 1.0.0 (2022-08-XX) ###
 
-This is a major release
+This is a major release of pairtools since last release (April 2019!)
 
-* parse
-- [x] parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109
-- [x] stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48 
-- [x] flipping issue: https://github.com/open2c/pairtools/issues/91 
+#### Post merge:
 
-Reporting:
-- pair types []
-- new fields
-- report all
+- [x] sphinx docs update with incorporated walkthroughs
 
-- changes in defaults
+#### New tools:
+- [x] parse2 module with CLI for parsing complex walks
+- [x] scaling and header modules with CLI
 
-* parse2
+#### Fixes by modules:
 
-* pairtools dedup
+pairtools dedup
 - [x] finalize detection of optical duplicates https://github.com/open2c/pairtools/issues/106 and https://github.com/open2c/pairtools/issues/59, also related to  https://github.com/open2c/pairtools/issues/54 
 - [x] chunked dedup by @Phlya 
 - [x] improvement of dedup to include reporting of the parent readID by @Phlya and @agalitsyna
 
-* dedup: implemented in chunks with two new backends ("scipy", "sklearn"). Now allows to
-  record the readID of the retained "parent" read from a duplicate cluster in an extra
-  field in the file with duplicates. New backends rely on the header to define column
-  oder in the file, specification through CLI arguments works for the "cython" backend,
-  but it will be removed in a future version.
-  Note that with non-zero max-mismatch the behaviour of the new backends can be
-  different from the old "cython": now duplication is transitive (i.e. if read A is a
-  duplicate of read B, and read B - of read C, reads A and C are now considered
-  duplicates).
-
-Note: this is the header post connecting multiple issues, feel free to update and improve!
-
-
 pairtools stats/scaling
 - [x] split dedup stats and regular stats
 - [x] output chromosome size to the stats output https://github.com/open2c/pairtools/issues/83 
 - [x] pairtools stats: YAML output? https://github.com/open2c/pairtools/issues/111  and https://github.com/open2c/pairtools/issues/79
 - [x] pairtools scaling tool which takes into account chromosome sizes: https://github.com/open2c/pairtools/issues/81,  https://github.com/open2c/pairtools/issues/56? 
 
+pairtools parse
+- [x] parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109
+- [x] stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48 
+- [x] flipping issue: https://github.com/open2c/pairtools/issues/91 
 
 pairtools phase
 - [x] make work with both pip and github versions of bwa: https://github.com/open2c/pairtools/pull/114
@@ -66,14 +53,12 @@ Code maintenance
 - [x] Clean up deprecation warnings, e.g. https://github.com/open2c/pairtools/issues/71
 - [x] Fix input errors without explanations, e.g. https://github.com/open2c/pairtools/issues/61 
 
-#### Specific proposals: 
+#### Specific changes: 
 
 Docs improvements
 - [x] pairtools walkthrough
 - [x] phasing walkthrough
 - [x] parse docs update
-- [x] sphinx docs update with incorporated walkthroughs
-
 
 Tests proposals
 - [x] add tests for dedup @Phlya : https://github.com/open2c/pairtools/issues/5
@@ -83,7 +68,8 @@ Enhancements
 - [x] add summaries: https://github.com/open2c/pairtools/pull/105 
 - [x] support of [bwa mem2]( https://github.com/bwa-mem2/bwa-mem2), which is 2-3 times faster than usual bwa mem: https://github.com/open2c/pairtools/discussions/118
 - [x] I/O single utility instead of repetitive code in each module
-
+
+
 ### 0.3.1 (2021-02-XX) ###
 
 * sample: a new tool to select a random subset of pairs

pairtools/__init__.py

@@ -10,6 +10,6 @@
 
 """
 
-__version__ = "1.0.0-dev1"
+__version__ = "1.0.0"
 
 # from . import lib