| f8ed3cb | Jerome Kelleher | 15 January 2018, 20:28:57 UTC | Merge pull request #350 from jeromekelleher/fix-setup Added missing comma to setup.py. | 15 January 2018, 20:28:57 UTC |
| 41418da | Jerome Kelleher | 15 January 2018, 20:16:50 UTC | Added missing comma to setup.py. | 15 January 2018, 20:16:50 UTC |
| cffec4f | Jerome Kelleher | 15 January 2018, 18:44:17 UTC | Merge pull request #346 from jeromekelleher/tables-docs Tables docs | 15 January 2018, 18:44:17 UTC |
| 4360ca7 | Jerome Kelleher | 15 January 2018, 17:48:00 UTC | Updated error messages. Closes #280. | 15 January 2018, 17:48:00 UTC |
| 491c94d | Jerome Kelleher | 15 January 2018, 17:33:00 UTC | Added example of using tables API to tutorial. Closes #292. | 15 January 2018, 17:33:00 UTC |
| 946a0c3 | Jerome Kelleher | 15 January 2018, 16:33:17 UTC | Added tree sequence requirements section. | 15 January 2018, 16:33:17 UTC |
| 9bf2d30 | Jerome Kelleher | 15 January 2018, 12:38:57 UTC | Documented MutationTable API and encoding functions. | 15 January 2018, 13:19:09 UTC |
| 2d20f56 | Jerome Kelleher | 15 January 2018, 12:08:11 UTC | Documented SiteTable API. | 15 January 2018, 12:08:11 UTC |
| 22bd465 | Jerome Kelleher | 15 January 2018, 11:51:01 UTC | Changed sphinx labels to use _ rather than -. This is so that vim will recognise the labels as identifiers and tab complete them. | 15 January 2018, 11:51:01 UTC |
| 51d11e2 | Jerome Kelleher | 15 January 2018, 11:26:58 UTC | Added example for ord("0") trick. | 15 January 2018, 11:26:58 UTC |
| 0ab7697 | Jerome Kelleher | 14 January 2018, 18:17:03 UTC | General docs for ragged columns. | 14 January 2018, 20:33:08 UTC |
| 8265395 | Jerome Kelleher | 13 January 2018, 12:26:21 UTC | Added docs for MigrationTable API. | 14 January 2018, 15:37:07 UTC |
| 63e8ff0 | Jerome Kelleher | 13 January 2018, 12:08:45 UTC | Updated EdgeTable API docs. | 14 January 2018, 15:37:07 UTC |
| 8f63bc4 | Jerome Kelleher | 14 January 2018, 15:32:24 UTC | Merge pull request #345 from jeromekelleher/workaround-windows Temporarily disable some threading tests on Windows. | 14 January 2018, 15:32:24 UTC |
| 41552b2 | Jerome Kelleher | 13 January 2018, 12:44:29 UTC | Temporarily disable some threading tests on Windows. | 13 January 2018, 12:44:29 UTC |
| 6ae8e09 | Jerome Kelleher | 13 January 2018, 12:41:04 UTC | Merge pull request #343 from jeromekelleher/tree-first Added TreeSequence.first() method. | 13 January 2018, 12:41:04 UTC |
| 1caf3ca | Jerome Kelleher | 13 January 2018, 11:47:47 UTC | Added TreeSequence.first() method. Closes #340. | 13 January 2018, 11:47:47 UTC |
| b9c7912 | Jerome Kelleher | 11 January 2018, 15:05:42 UTC | Merge pull request #339 from jeromekelleher/strict-text Text formats update. | 11 January 2018, 15:05:42 UTC |
| f169612 | Jerome Kelleher | 11 January 2018, 14:19:59 UTC | Updated documentation for text formats. | 11 January 2018, 14:19:59 UTC |
| 3f14e89 | Jerome Kelleher | 11 January 2018, 12:33:06 UTC | Change 'sep' argument to 'strict'. Closes #337. | 11 January 2018, 12:33:06 UTC |
| 9c4ea66 | Jerome Kelleher | 10 January 2018, 17:56:48 UTC | Merge pull request #335 from jeromekelleher/docathon Update docs for tables API. | 10 January 2018, 17:56:48 UTC |
| a35a4c2 | Jerome Kelleher | 10 January 2018, 16:30:12 UTC | Added more detail to the table definitions. | 10 January 2018, 16:37:24 UTC |
| 84c4212 | Jerome Kelleher | 10 January 2018, 14:14:08 UTC | Added discussion of pickle and == support for tables. | 10 January 2018, 14:14:08 UTC |
| 358f188 | Jerome Kelleher | 10 January 2018, 13:56:54 UTC | Changed Table.reset() to Table.clear(). This is a more Pythonic naming convention. Table.reset() has been retained as a deprecated alias. | 10 January 2018, 13:56:54 UTC |
| 853e11a | Jerome Kelleher | 09 January 2018, 17:03:57 UTC | Moved the table example to the section header. | 09 January 2018, 17:03:57 UTC |
| 6b8349a | Jerome Kelleher | 09 January 2018, 15:58:46 UTC | Changed high-level method signatures, update docs. | 09 January 2018, 15:58:46 UTC |
| 5d30366 | Jerome Kelleher | 08 January 2018, 21:00:31 UTC | Added row access to remaining tables. | 08 January 2018, 21:00:31 UTC |
| f27ba6e | Jerome Kelleher | 08 January 2018, 16:55:43 UTC | Add row-access for NodeTable. | 08 January 2018, 16:55:43 UTC |
| 0c58c5b | Jerome Kelleher | 08 January 2018, 15:50:44 UTC | Improvements to Tables API: 1. add_row now returns the ID of the row just added. 2. Metadata now defaults to None, making documentation of high-level methods easier. 3. Partial updates of the high-level tables API methods. | 08 January 2018, 16:15:11 UTC |
| a551699 | Jerome Kelleher | 03 January 2018, 13:20:22 UTC | Changed sphinx docs to Python3 only. Also added manual mocks so that API docs show up. | 03 January 2018, 14:42:20 UTC |
| 1b8105f | Jerome Kelleher | 02 January 2018, 19:29:33 UTC | reorganising tables API docs. | 03 January 2018, 14:42:07 UTC |
| 6616838 | Jerome Kelleher | 02 January 2018, 18:16:52 UTC | Updated HDF5 format definitions for v10. | 03 January 2018, 10:22:37 UTC |
| e044d3d | Jerome Kelleher | 03 January 2018, 10:21:31 UTC | Merge pull request #333 from jeromekelleher/text-metadata Text metadata | 03 January 2018, 10:21:31 UTC |
| 6a80764 | Jerome Kelleher | 01 January 2018, 20:14:35 UTC | Fixup sort_tables and tests. | 03 January 2018, 09:50:43 UTC |
| c033d63 | Jerome Kelleher | 01 January 2018, 17:48:48 UTC | Added general separator argument to load_text. | 03 January 2018, 09:50:43 UTC |
| 198d31a | Jerome Kelleher | 01 January 2018, 16:50:39 UTC | Fixed erroneous assert. | 03 January 2018, 09:50:43 UTC |
| b5a3184 | Jerome Kelleher | 01 January 2018, 16:18:03 UTC | Added base64 encoding of metadata for text format. | 03 January 2018, 09:50:43 UTC |
| fd06d69 | Jerome Kelleher | 02 January 2018, 18:01:48 UTC | Merge pull request #334 from ashander/document-load-tables Docstring updates: load_tables, simplify_tables, EdgeTable | 02 January 2018, 18:01:48 UTC |
| 82dece2 | Jaime Ashander | 02 January 2018, 17:11:04 UTC | Fix arglist in simplify_tables doc | 02 January 2018, 17:11:04 UTC |
| 9524e8b | Jaime Ashander | 02 January 2018, 04:11:16 UTC | Improve docs for Tables API Additions or fixes in: load_tables, sort_tables, simplify_tables, dump_tables, and EdgeTable | 02 January 2018, 17:02:21 UTC |
| 3f44cba | Jerome Kelleher | 21 December 2017, 14:11:42 UTC | Merge pull request #330 from jeromekelleher/binary-metadata Basic examples for json-schema metadata. | 21 December 2017, 14:11:42 UTC |
| 3c2caba | Jerome Kelleher | 21 December 2017, 12:50:03 UTC | Basic examples for json-schema metadata. | 21 December 2017, 13:39:40 UTC |
| d09cc6d | Jerome Kelleher | 21 December 2017, 11:28:09 UTC | Merge pull request #328 from jeromekelleher/variant-alleles Add 'alleles' list to Variant object. | 21 December 2017, 11:28:09 UTC |
| 4871308 | Jerome Kelleher | 21 December 2017, 11:00:10 UTC | Added checks for large numbers of alleles. | 21 December 2017, 11:00:10 UTC |
| eb2b1d9 | Jerome Kelleher | 20 December 2017, 16:45:16 UTC | Removed mutations from WF simulator; use jukes_cantor instead. | 20 December 2017, 16:45:16 UTC |
| 358cdb5 | Jerome Kelleher | 20 December 2017, 15:45:02 UTC | Tests for multi-char mutations & fix simplify bug. | 20 December 2017, 16:19:00 UTC |
| 22e4225 | Jerome Kelleher | 20 December 2017, 12:38:44 UTC | Initial support for variant.alleles. | 20 December 2017, 12:38:44 UTC |
| b87748c | Jerome Kelleher | 20 December 2017, 11:45:00 UTC | Removed buffer from VariantGenerator and simplified. | 20 December 2017, 11:45:00 UTC |
| 38df8e2 | Jerome Kelleher | 20 December 2017, 10:12:24 UTC | Fixed missing genotypes copy. | 20 December 2017, 10:12:24 UTC |
| 88bafb2 | Jerome Kelleher | 20 December 2017, 09:47:20 UTC | Fixed some flake8 issues. | 20 December 2017, 09:47:20 UTC |
| 3d99916 | Jerome Kelleher | 19 December 2017, 19:03:55 UTC | Minimal changes to make variant generator work. | 19 December 2017, 19:07:04 UTC |
| 6b0fa7b | Jerome Kelleher | 19 December 2017, 18:46:50 UTC | Removed 'alphabet' concept and binary haplotype generator. | 19 December 2017, 18:46:50 UTC |
| 2dad459 | Jerome Kelleher | 19 December 2017, 18:31:06 UTC | Basic low-level changes needed for variants/alleles. | 19 December 2017, 18:31:06 UTC |
| f9a7313 | Jerome Kelleher | 19 December 2017, 14:09:59 UTC | Initial pass at alleles for variant generator. | 19 December 2017, 14:09:59 UTC |
| a267e1c | Jerome Kelleher | 16 December 2017, 13:20:00 UTC | Merge pull request #326 from ashander/tag-file-format-version Add listing of hdf5 file formats to docs | 16 December 2017, 13:20:00 UTC |
| 33c1abc | Jaime Ashander | 06 December 2017, 23:51:00 UTC | Document hdf5 format versions raw data created with git log --oneline -L40,41:lib/msprime.h > raw_data.txt | 15 December 2017, 21:08:17 UTC |
| 6de8ed1 | Jerome Kelleher | 13 December 2017, 09:39:48 UTC | Merge pull request #322 from jeromekelleher/ragged_col_cumulative Change ragged column lengths to offsets | 13 December 2017, 09:39:48 UTC |
| ae9bb7b | Jerome Kelleher | 12 December 2017, 14:50:56 UTC | Initial mutation metadata API. | 12 December 2017, 14:53:10 UTC |
| b60a54b | Jerome Kelleher | 12 December 2017, 14:32:11 UTC | Changed simplify_tables to return node_map. This fixes a potential memory access violation under threads and simplifies the API. | 12 December 2017, 14:32:11 UTC |
| 3eadf15 | Jerome Kelleher | 12 December 2017, 13:14:59 UTC | Fixed memory leak from HDF5 version, and GIL issue. | 12 December 2017, 13:14:59 UTC |
| dfe6a29 | Jerome Kelleher | 12 December 2017, 11:05:04 UTC | Initial changes for mutation.metadata. | 12 December 2017, 11:05:04 UTC |
| 375add1 | Jerome Kelleher | 12 December 2017, 10:29:42 UTC | Low-level changes for mutation.metadata. | 12 December 2017, 10:50:17 UTC |
| ae6e2e5 | Jerome Kelleher | 11 December 2017, 20:42:09 UTC | Finished high-level changes for site metadata. | 11 December 2017, 20:59:23 UTC |
| 6189577 | Jerome Kelleher | 11 December 2017, 15:46:14 UTC | Low-level implementation of site metadata. | 11 December 2017, 17:47:14 UTC |
| bde116c | Jerome Kelleher | 11 December 2017, 13:45:02 UTC | Changed list_len_t to table_size_t. | 11 December 2017, 15:52:02 UTC |
| 32283cc | Jerome Kelleher | 08 December 2017, 17:00:23 UTC | Cleared up various testing issues and gaps. | 09 December 2017, 19:58:51 UTC |
| 7d007af | Jerome Kelleher | 08 December 2017, 16:06:59 UTC | Updated HDF5 format tests. | 08 December 2017, 16:06:59 UTC |
| 6d5e14c | Jerome Kelleher | 08 December 2017, 15:04:56 UTC | Added basic output for provenances. | 08 December 2017, 15:04:56 UTC |
| 9b41c8a | Jerome Kelleher | 08 December 2017, 14:25:26 UTC | Updated low-level Python provenance API. | 08 December 2017, 14:25:26 UTC |
| 496df9d | Jerome Kelleher | 08 December 2017, 12:31:06 UTC | Changed provenance to provenances for consistency. | 08 December 2017, 12:31:06 UTC |
| e7c7240 | Jerome Kelleher | 08 December 2017, 12:29:20 UTC | Updated low-level APIs for provenance. | 08 December 2017, 12:29:20 UTC |
| 43aada8 | Jerome Kelleher | 08 December 2017, 11:05:29 UTC | Changed Provenance.provenance to Provenance.record. | 08 December 2017, 11:05:29 UTC |
| a1c0bf2 | Jerome Kelleher | 08 December 2017, 10:02:32 UTC | Added ID column to node text format. Removed dump_sample_text method. | 08 December 2017, 10:02:32 UTC |
| 2341f23 | Jerome Kelleher | 08 December 2017, 09:22:06 UTC | Fixed memory leak in table pickling. | 08 December 2017, 09:22:06 UTC |
| 195d13b | Jerome Kelleher | 07 December 2017, 17:18:13 UTC | Removed 'restrict' keyword as caused problems. | 07 December 2017, 17:18:13 UTC |
| 4f66d8f | Jerome Kelleher | 07 December 2017, 17:05:42 UTC | Rough high-level changes for ProvenanceTable. | 07 December 2017, 17:05:42 UTC |
| b862cd0 | Jerome Kelleher | 07 December 2017, 15:36:11 UTC | Made tests compile and pass for provenance changes. | 07 December 2017, 15:36:11 UTC |
| 6f091b2 | Jerome Kelleher | 07 December 2017, 15:21:11 UTC | Initial changeover to provenance table. | 07 December 2017, 15:21:11 UTC |
| b4b3d3a | Jerome Kelleher | 07 December 2017, 11:45:11 UTC | Fixed py3 test bug, and improved bytes encoder. | 07 December 2017, 11:45:11 UTC |
| ec8a7c2 | Jerome Kelleher | 07 December 2017, 11:18:24 UTC | Make py3 default makefile target. | 07 December 2017, 11:18:24 UTC |
| a315662 | Jerome Kelleher | 06 December 2017, 20:55:06 UTC | Initial addition of provenance_table_t. | 06 December 2017, 20:55:06 UTC |
| 5ad4311 | Jerome Kelleher | 06 December 2017, 20:08:27 UTC | Fixed bug in metadata recording. | 06 December 2017, 20:08:27 UTC |
| 4b697e4 | Jerome Kelleher | 06 December 2017, 17:55:55 UTC | Initial coding for metadata on nodes. | 06 December 2017, 17:55:55 UTC |
| 0fcffe9 | Jerome Kelleher | 06 December 2017, 16:48:03 UTC | Added methods to pack binary data. | 06 December 2017, 16:48:03 UTC |
| be36662 | Jerome Kelleher | 05 December 2017, 21:01:59 UTC | Cast to Py_ssize_t for 64 bit windows. | 05 December 2017, 21:01:59 UTC |
| b1f0e83 | Jerome Kelleher | 05 December 2017, 20:52:47 UTC | Changed node.name to node.metadata. | 05 December 2017, 20:52:47 UTC |
| 8ebecab | Jerome Kelleher | 05 December 2017, 20:30:44 UTC | name->metadata in C code. | 05 December 2017, 20:30:44 UTC |
| f68f7fd | Jerome Kelleher | 29 November 2017, 14:52:08 UTC | Change tables API to use offset arrays instead of length. This commit changes the protocol used to encoded ragged length arrays in the tables API to use an array of n + 1 offsets to encode n variable length rows. The HDF5 format versino has been bumped but not finalised. | 05 December 2017, 20:11:06 UTC |
| e504abd | Jerome Kelleher | 04 December 2017, 10:38:48 UTC | Merge pull request #324 from jeromekelleher/update-pep8 Fix minor flake8 issues. | 04 December 2017, 10:38:48 UTC |
| da67e3f | Jerome Kelleher | 04 December 2017, 10:07:38 UTC | Fix minor flake8 issues. | 04 December 2017, 10:07:38 UTC |
| c85ac01 | Jerome Kelleher | 30 November 2017, 16:31:41 UTC | Merge pull request #321 from ashander/update-docs-to-tables Update EdgeTable and NodeTable docstrings/docs | 30 November 2017, 16:31:41 UTC |
| 8d659b6 | Jaime Ashander | 28 November 2017, 20:53:43 UTC | Updating EdgeTable and NodeTable docs | 29 November 2017, 17:16:20 UTC |
| 5ccbeec | Jerome Kelleher | 27 November 2017, 19:50:07 UTC | Merge pull request #320 from jeromekelleher/simplify-gil Release GIL during table operations. | 27 November 2017, 19:50:07 UTC |
| 29a1328 | Jerome Kelleher | 27 November 2017, 13:25:57 UTC | Changed failure threshold for thread tests to >= 0. It's too difficult to require this and will lead to random failures on CI. | 27 November 2017, 13:25:57 UTC |
| bc0c38d | Jerome Kelleher | 25 November 2017, 13:52:58 UTC | Fixed logic bug in lock release and updated tests. | 25 November 2017, 13:52:58 UTC |
| ffc7671 | Jerome Kelleher | 22 November 2017, 12:30:12 UTC | Release GIL during table operations. Adds a 'lock' to each table object, which should ensure thread safety in Python. Any access to a table operate which changes its state should set these locks before releasing the GIL. | 22 November 2017, 12:30:12 UTC |
| a92660a | Jerome Kelleher | 21 November 2017, 19:46:55 UTC | Merge pull request #319 from jeromekelleher/simplify-perf-notes Added note on performance impact of defrag. | 21 November 2017, 19:46:55 UTC |
| a7c3091 | Jerome Kelleher | 21 November 2017, 17:23:29 UTC | Added notes on performance for simplify. | 21 November 2017, 17:54:01 UTC |
| 4e0e05e | Jerome Kelleher | 21 November 2017, 09:48:02 UTC | Merge pull request #318 from petrelharp/print_nodes print node table prints `is_sample` instead of `flags` | 21 November 2017, 09:48:02 UTC |
| bb8eaef | peter | 20 November 2017, 21:37:04 UTC | print node table uses is_sample not flags | 20 November 2017, 21:37:04 UTC |
