Merge pull request #53 from adalke/v3-dev

V3 dev -> mmpdb 3.1

Author: chem-bio

CHANGELOG.md

@@ -1,6 +1,69 @@
 # CHANGELOG
 
-## mmpdb (in development)
+## mmpdb 3.1 - 2023-11-28
+
+Extended the "generate" command to handle 2-, and 3-cut transforms.
+
+The `generate --explain` option now also explains why the search for a
+matching query or variable part passes or fails. This proved useful in
+determining that an expected fragmentation was instead being filtered.
+
+The new `--min-heavies-total-const-frag N` fragmentation option
+specifies the minimum number of heavy atoms allowed in the constant
+part. The default value is 0.
+
+Changed the fragdb schema version (in the "options" table) from 3 to 4
+to support the new fragmentation option. Version 3 fragment databases
+are still supported, by `min_heavies_total_const_frag` to 0.
+
+Added two indices and a SQLite pragma for the page size. Roche reports
+these improve analysis performance.
+
+Fixed `--from` and `--to` support in proprulecat. These had been left
+behind in the migration to click from argparse for command-line
+processing.
+
+## mmpdb 3.0 - 2023-5-31 
+
+A large number of changes to merge three different development tracks
+and add new features.
+
+The "fragments" file format has been replaced with a SQLite-based
+"fragdb" file format. This makes it much easier to develop tools to
+work on fragment data sets instead of processing a JSON-Lines file.
+
+New functionality to create an MMP data set in a distributed compute
+environment. Some of the features are:
+
+- split a SMILES file into a set of smaller SMILES files
+- the default "fragment" file output is now based on the input name
+- fragment files can be re-partitioned by constant fragments:
+    - the "fragdb_constants" file generates fragment information
+    - the "fragdb_partition" create re-partitioned fragdb files
+- the default "index" file output is now based on the input name
+- there are tools to merge fragdb and mmpdb files into one
+
+As a result, mmpdb can now handle significantly larger data sets.
+
+Added support for Postgres for direct index database creation. (The
+new distributed compute tools require SQLite.)
+
+Added a new "generate" command to apply 1-cut transforms to a
+structure, using MMP rules as a playbook.
+
+Replaced the SHA256-based Morgan fingerprint signature with a
+canonical SMARTS representing the Morgan fingerprint environment. This
+is difficult to understand or depict, so also include a "pseudo"
+SMILES that can be parsed by RDKit (if sanitize is disabled) and
+drawn. The new environment fingerprint also include the SMARTS of its
+parent, that is, the SMARTS with a smaller radius.
+
+Switched to 'click' for command-line parsing, removed the vendered
+version of the peewee ORM, and switched to a modern "pyproject.toml"
+project configuration with a setup.cfg which declares its dependencies.
+
+
+## mmpdb 2.2-dev (the GitHub development track)
 
 The `fragment` and `smifrag` commands now support options for
 supervised fragmentation based on a specified set of R-group SMILES to

MANIFEST

@@ -40,15 +40,15 @@ mmpdblib/playhouse/db_url.py
 mmpdblib/playhouse/flask_utils.py
 mmpdblib/playhouse/pool.py
 mmpdblib/playhouse/sqlite_ext.py
-tests/cached.fragments
+tests/cached.fragdb
 tests/comma.smi
 tests/space.smi
 tests/space.smi.gz
 tests/support.py
 tests/tab.smi
 tests/test_analysis.py
 tests/test_data.csv
-tests/test_data.fragments
+tests/test_data.fragdb
 tests/test_data.mmpdb
 tests/test_data.smi
 tests/test_data_2018.mmpdb

MANIFEST.in

@@ -5,43 +5,8 @@ include CHANGELOG.md
 include mmpdb
 include setup.py
 include setup.cfg
-include mmpdblib/__init__.py
-include mmpdblib/__main__.py
-include mmpdblib/_compat.py
-include mmpdblib/analysis_algorithms.py
-include mmpdblib/cansmirks_table.py
-include mmpdblib/command_support.py
-include mmpdblib/commandline.py
-include mmpdblib/config.py
-include mmpdblib/create_index.sql
-include mmpdblib/dbutils.py
-include mmpdblib/do_analysis.py
-include mmpdblib/do_database.py
-include mmpdblib/do_fragment.py
-include mmpdblib/do_help.py
-include mmpdblib/do_index.py
-include mmpdblib/drop_index.sql
-include mmpdblib/environment.py
-include mmpdblib/fileio.py
-include mmpdblib/frag2smarts.py
-include mmpdblib/fragment_algorithm.py
-include mmpdblib/fragment_io.py
-include mmpdblib/fragment_types.py
-include mmpdblib/index_algorithm.py
-include mmpdblib/index_writers.py
-include mmpdblib/peewee.py
-include mmpdblib/properties_io.py
-include mmpdblib/reporters.py
-include mmpdblib/schema.py
-include mmpdblib/schema.sql
-include mmpdblib/smarts_aliases.py
-include mmpdblib/smiles_syntax.py
-include mmpdblib/playhouse/__init__.py
-include mmpdblib/playhouse/apsw_ext.py
-include mmpdblib/playhouse/db_url.py
-include mmpdblib/playhouse/flask_utils.py
-include mmpdblib/playhouse/pool.py
-include mmpdblib/playhouse/sqlite_ext.py
+include pyproject.toml
+recursive-include mmpdb *.py
 
 include tests/cached.fragments
 include tests/comma.smi