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https://github.com/dhimmel/hetio
12 April 2020, 02:22:18 UTC
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Revision Author Date Message Commit Date
02e6f77 Daniel Himmelstein 15 August 2018, 19:27:11 UTC Upgrade to v0.2.9 15 August 2018, 19:27:11 UTC
2fe1c30 Daniel Himmelstein 15 August 2018, 19:18:06 UTC Document hetio.permute functions Merges https://github.com/hetio/hetio/pull/24 15 August 2018, 19:18:06 UTC
958b0ae Daniel Himmelstein 09 August 2018, 19:37:41 UTC Relocate repo from dhimmel/hetio to hetio/hetio Merges https://github.com/hetio/hetio/pull/23 09 August 2018, 19:37:41 UTC
4657926 Daniel Himmelstein 08 August 2018, 14:44:41 UTC Travis config: fix indent 08 August 2018, 14:44:41 UTC
f5dd406 Daniel Himmelstein 03 August 2018, 21:09:33 UTC Remove ignored Travis deploy option From https://docs.travis-ci.com/user/deployment > tags: true: deployment is triggered if and only if $TRAVIS_TAG is set. Depending on your workflow, you may set $TRAVIS_TAG explicitly, even if this is a non-tag build when it was initiated. This causes the branch condition to be ignored. 03 August 2018, 21:09:33 UTC
f2e525a Daniel Himmelstein 07 June 2018, 17:16:30 UTC Enable edge/path sorting Merges https://github.com/dhimmel/hetio/pull/22 * Enable edge/path sorting * Enable deterministic extract_metapaths ordering * Test metapath sorting 07 June 2018, 17:16:30 UTC
1c69ce4 Daniel Himmelstein 04 June 2018, 16:23:18 UTC graph.count_nodes & matrix.get_node_identifiers functions (#21) Merges https://github.com/dhimmel/hetio/pull/21 * Add count_nodes function * Add matrix.get_node_identifiers 04 June 2018, 16:23:18 UTC
aa58b2b Michael Zietz 01 June 2018, 20:14:07 UTC Optimize matrix.sparsify_or_densify Merges https://github.com/dhimmel/hetio/pull/20 Use scipy.sparse nnz attribute to avoid a potentially expensive computation of the number of nonzeros in a sparse matrix. 01 June 2018, 20:14:07 UTC
100e9e5 Daniel Himmelstein 18 May 2018, 21:59:25 UTC Convenience function: metagraph.get_metapath Squash merges https://github.com/dhimmel/hetio/pull/19 18 May 2018, 21:59:25 UTC
6e7ee73 Daniel Himmelstein 15 May 2018, 19:20:44 UTC MetaGraph: metanode and metaedge getter methods Merges https://github.com/dhimmel/hetio/pull/18 Add metanode and metaedge getters for convenience: - metagraph.get_metanode - metagraph.get_metaedge 15 May 2018, 19:40:06 UTC
4786dae Michael Zietz 10 May 2018, 14:55:07 UTC sparsify_or_densify: workaround scipy float16 todense bug Merges https://github.com/dhimmel/hetio/pull/15 Update sparsify_or_densify to workaround https://github.com/scipy/scipy/issues/7408 whereby float16 sparse matrices do not convert to dense arrays. 10 May 2018, 14:55:07 UTC
9d9ef13 Daniel Himmelstein 24 April 2018, 20:10:31 UTC setup.py: PyPI now supports markdown long_description 24 April 2018, 20:10:31 UTC
aa5d12e Daniel Himmelstein 06 April 2018, 16:49:19 UTC extract_all_metapaths: get all metapaths for any source/target metanodes Merges https://github.com/dhimmel/hetio/pull/14 Motivated by https://github.com/greenelab/hetmech/issues/76#issuecomment-378698413 Changes metapath.extract_metapaths in a non-backwards compatible way: argument names have changed, positions have stayed the same. Enables target=None for all metaptahs starting on source. 06 April 2018, 16:49:19 UTC
3156ab1 Daniel Himmelstein 05 April 2018, 20:50:14 UTC Simplify .gitignore 05 April 2018, 20:50:14 UTC
21c6443 Daniel Himmelstein 05 April 2018, 20:43:54 UTC readwrite: support pathlike objects 05 April 2018, 20:45:59 UTC
f60f95d Daniel Himmelstein 04 April 2018, 21:26:28 UTC DOC: abbreviation regex pattern comment 04 April 2018, 21:26:28 UTC
98564d6 Greg Way 04 April 2018, 19:25:18 UTC Enable digits in metanode abbreviations Merges https://github.com/dhimmel/hetio/pull/13 Closes https://github.com/dhimmel/hetio/issues/12 Metanodes abbreviations can now contain digits as long as the first character is an uppercase letter. Test abbreviation.metaedges_from_metapath and test for digits in abbreviation.validate_abbreviations. 04 April 2018, 19:25:18 UTC
ddc655c Daniel Himmelstein 27 March 2018, 14:36:44 UTC Upgrade to v0.2.8 27 March 2018, 14:36:44 UTC
7f33036 Daniel Himmelstein 27 March 2018, 14:31:59 UTC Merge PR: matrix code from greenelab/hetmech Migrate hetnet to matrix code from greenelab/hetmech Merges https://github.com/dhimmel/hetio/pull/11 27 March 2018, 14:31:59 UTC
d3d66b5 Daniel Himmelstein 26 March 2018, 20:44:50 UTC Rename fxn to sparsify_or_densify & tests 27 March 2018, 14:26:01 UTC
c21189f Daniel Himmelstein 26 March 2018, 15:47:37 UTC Refine matrix code & incoporate into hetio 27 March 2018, 14:26:01 UTC
fc7f108 Michael Zietz 26 March 2018, 14:43:09 UTC Copy matrix.py + tests from greenelab/hetmech Sources: https://github.com/greenelab/hetmech/blob/fdcf40b4771237a24b73a91446e6e04dded97455/hetmech/matrix.py https://github.com/greenelab/hetmech/blob/fdcf40b4771237a24b73a91446e6e04dded97455/hetmech/test_matrix.py 26 March 2018, 15:28:07 UTC
ed400ff Daniel Himmelstein 15 February 2018, 15:25:07 UTC Upgrade to v0.2.7 15 February 2018, 15:25:07 UTC
9f66bd4 Daniel Himmelstein 22 September 2017, 19:14:38 UTC Update README with eLife publication 22 September 2017, 19:14:38 UTC
30c6dbb Daniel Himmelstein 01 June 2017, 19:36:24 UTC Create Hetionet v1.0 subgraph with all metanodes 01 June 2017, 19:36:24 UTC
62c4dd1 Daniel Himmelstein 31 May 2017, 18:13:10 UTC Fix AttributeError in metapath.get_unicode_str() https://github.com/dhimmel/hetio/commit/9dc747b8fc4e23ef3437829ffde4d047f2e1bdde broke get_unicode_str for metapaths whose names did not contain a name attribute. Fixes: AttributeError: 'MetaNode' object has no attribute 'name' 31 May 2017, 18:13:10 UTC
c1d47a9 Daniel Himmelstein 31 May 2017, 15:53:48 UTC Test traversal on CbGpPWpGaD subgraph 31 May 2017, 15:53:48 UTC
e72e513 Daniel Himmelstein 31 May 2017, 15:53:03 UTC Improve kind_to_abbrev subsetting in get_subgraph 31 May 2017, 15:53:03 UTC
dcb04eb Daniel Himmelstein 30 May 2017, 17:08:53 UTC get_subgraph to subset hetnets 30 May 2017, 18:50:05 UTC
86c1114 Daniel Himmelstein 20 April 2017, 15:55:41 UTC Specify python_requires in setup.py 20 April 2017, 15:55:41 UTC
56f6262 Daniel Himmelstein 04 April 2017, 20:08:44 UTC Upgrade to v0.2.6 04 April 2017, 20:08:44 UTC
f7b6ccb Daniel Himmelstein 04 April 2017, 20:06:48 UTC TST: test GeTlD metapath in gene-disease example 04 April 2017, 20:06:48 UTC
2562850 Daniel Himmelstein 01 April 2017, 20:34:07 UTC Style: flake8 abbreviation.py 01 April 2017, 20:34:07 UTC
13436b2 Daniel Himmelstein 01 April 2017, 20:23:40 UTC Style: flake8 pathtools.py 01 April 2017, 20:23:40 UTC
a7aaded Daniel Himmelstein 01 April 2017, 19:33:10 UTC Fix node __repr__ in notebook 01 April 2017, 19:33:10 UTC
9dc747b Daniel Himmelstein 01 April 2017, 18:14:58 UTC Doc & Style: flake8 and docstrings 01 April 2017, 18:17:08 UTC
4591708 Daniel Himmelstein 01 April 2017, 18:03:04 UTC Add PC / DWPC test 01 April 2017, 18:03:04 UTC
a0e904a Daniel Himmelstein 01 April 2017, 17:45:03 UTC BUG: add missing edges, fix path name In disease-gene-example-graph test 01 April 2017, 17:59:07 UTC
1045b84 Daniel Himmelstein 01 April 2017, 17:35:19 UTC Style: flake8 graph_test.py 01 April 2017, 17:35:19 UTC
7eedc98 Daniel Himmelstein 01 April 2017, 17:30:06 UTC TST: create example disease-gene graph Hetnet from https://doi.org/10.1371/journal.pcbi.1004259.g002 01 April 2017, 17:30:06 UTC
46a6b09 Daniel Himmelstein 01 April 2017, 17:03:38 UTC ENH: support source/target node in add_edge 01 April 2017, 17:03:38 UTC
0b3ccb7 Daniel Himmelstein 28 March 2017, 14:43:07 UTC Upgrade to v0.2.5 28 March 2017, 14:43:07 UTC
f284014 Daniel Himmelstein 28 March 2017, 14:42:46 UTC Fix README command for __version__ 28 March 2017, 14:42:46 UTC
558e379 Daniel Himmelstein 28 March 2017, 13:51:44 UTC Travis: github releases use @hetio-release-bot 28 March 2017, 13:51:44 UTC
488d603 Daniel Himmelstein 18 March 2017, 21:06:18 UTC Add hetio.__version__ support See https://packaging.python.org/single_source_version/ 18 March 2017, 21:06:18 UTC
525837a Daniel Himmelstein 17 March 2017, 21:15:42 UTC Upgrade to v0.2.4 17 March 2017, 21:15:42 UTC
a7c2755 Daniel Himmelstein 17 March 2017, 21:02:10 UTC Style: satisfy flake8 in hetio.readwrite 17 March 2017, 21:02:10 UTC
421860c Daniel Himmelstein 17 March 2017, 20:48:18 UTC Remove yaml readwrite support 17 March 2017, 20:59:56 UTC
f21a73b Daniel Himmelstein 17 March 2017, 19:45:00 UTC Remove requests dependency. Test metagraph reading Remove examples since metagraphs move to test/data. 17 March 2017, 19:56:58 UTC
432f14b Daniel Himmelstein 16 March 2017, 17:45:39 UTC Reformat setup.py. Configure extras_require 16 March 2017, 17:45:39 UTC
3e236ef Daniel Himmelstein 16 March 2017, 17:28:42 UTC Improve hetio.hetnet style 16 March 2017, 17:28:42 UTC
4f5bfa5 Daniel Himmelstein 03 March 2017, 01:49:20 UTC Add release instructions 03 March 2017, 01:57:06 UTC
1e00ce4 Daniel Himmelstein 03 March 2017, 01:03:50 UTC Upgrade to v0.2.3 03 March 2017, 01:03:50 UTC
24b2036 Daniel Himmelstein 03 March 2017, 00:15:14 UTC Upgrade Travis to Trusty for newer Pandoc Use Ubuntu 14.04 with Pandoc 1.12.2. Fixes pandoc rst bug which was responsible for the ugly README in https://pypi.org/project/hetio/0.2.2/ 03 March 2017, 00:42:44 UTC
f742a96 Daniel Himmelstein 02 March 2017, 23:57:34 UTC Upgrade to v0.2.2 02 March 2017, 23:57:34 UTC
cbfd4c3 Daniel Himmelstein 02 March 2017, 23:42:23 UTC Travis PyPI deploy: add wheel 02 March 2017, 23:46:45 UTC
2587193 Daniel Himmelstein 02 March 2017, 23:34:01 UTC Limit deployment to Python 3.6 job only 02 March 2017, 23:34:01 UTC
a34946f Daniel Himmelstein 02 March 2017, 23:29:01 UTC Remove register.py, switching to Travis deploy 02 March 2017, 23:29:01 UTC
8858d78 Daniel Himmelstein 02 March 2017, 23:19:48 UTC Travis CI: deploy to PyPI 02 March 2017, 23:23:09 UTC
0b7baab Daniel Himmelstein 02 March 2017, 23:07:00 UTC Travis CI: deploy to GitHub Releases 02 March 2017, 23:23:09 UTC
8f74660 Daniel Himmelstein 02 March 2017, 22:43:38 UTC Use pandoc to generate README.rst Closes https://github.com/dhimmel/hetio/issues/7 02 March 2017, 22:47:41 UTC
91562f7 Daniel Himmelstein 02 March 2017, 22:10:21 UTC Expand setup.py lists 02 March 2017, 22:10:21 UTC
d026d13 Tong Shu Li 02 March 2017, 21:39:57 UTC Change neo4j import queue size defaults Intended to speed up the hetnet importation into Neo4j. See https://github.com/dhimmel/hetio/issues/5 02 March 2017, 21:39:57 UTC
bf8f548 Daniel Himmelstein 02 March 2017, 21:36:53 UTC Minor cleaning of neo4j.py 02 March 2017, 21:36:53 UTC
7fe01f1 Tong Shu Li 02 March 2017, 21:28:39 UTC Add py2neo version 3 URI compatibility (#8) Closes https://github.com/dhimmel/hetio/issues/4 Closes https://github.com/dhimmel/hetio/pull/8 Closes https://github.com/dhimmel/hetio/pull/6 02 March 2017, 21:28:39 UTC
48b65b0 Daniel Himmelstein 16 February 2017, 00:28:25 UTC Disable failing pytest feature in travis py34 16 February 2017, 00:28:25 UTC
d32ba2a Daniel Himmelstein 16 February 2017, 00:23:24 UTC Add support for bidirectional self-loop edges Do not allow the adding of duplicate edges. 16 February 2017, 00:23:24 UTC
8531e2b Daniel Himmelstein 15 February 2017, 23:35:03 UTC Improve tests 15 February 2017, 23:35:03 UTC
7472d90 Daniel Himmelstein 15 February 2017, 23:06:00 UTC Make abbreviation tests pytest discoverable 15 February 2017, 23:06:00 UTC
0799fe3 Daniel Himmelstein 15 February 2017, 22:28:42 UTC Add Travis CI 15 February 2017, 22:35:59 UTC
903a4c8 Daniel Himmelstein 15 February 2017, 22:18:32 UTC Count nodes and edges in graph 15 February 2017, 22:18:32 UTC
69aea62 Daniel Himmelstein 15 February 2017, 22:17:16 UTC Fix tests with updated import path 15 February 2017, 22:17:16 UTC
042ba59 Daniel Himmelstein 29 September 2016, 00:48:20 UTC Add pip install from PyPi command 29 September 2016, 00:48:20 UTC
321fc74 Daniel Himmelstein 29 September 2016, 00:47:11 UTC Move pypandoc to dev but not install dependency Upload to PyPI as v0.2.1. register.py performs upload 29 September 2016, 00:47:11 UTC
ace55ab Daniel Himmelstein 05 September 2016, 19:45:59 UTC Prepare 0.2.0 release and ready for PyPI 05 September 2016, 19:45:59 UTC
63a3737 Daniel Himmelstein 05 September 2016, 17:23:41 UTC Add get_unicode_str function to BasePath 05 September 2016, 17:23:41 UTC
6d4a6f9 Daniel Himmelstein 20 May 2016, 18:22:39 UTC Check type for edge/path equality 20 May 2016, 18:22:39 UTC
2c135fc Daniel Himmelstein 30 March 2016, 18:15:03 UTC Add unicode metaedge str and style dataframe 30 March 2016, 18:15:03 UTC
7542a0d Daniel Himmelstein 22 March 2016, 05:28:33 UTC Fix empty labeled unique node constraint bug 22 March 2016, 05:28:33 UTC
4a492cd Daniel Himmelstein 21 March 2016, 20:32:25 UTC Separate index and join hints 21 March 2016, 20:32:25 UTC
9517fd4 Daniel Himmelstein 18 March 2016, 05:11:26 UTC Fix non-xlsxwriter engine error 18 March 2016, 05:11:26 UTC
7ecb8c9 Daniel Himmelstein 18 March 2016, 00:44:11 UTC Fix metanodes with no nodes bug 18 March 2016, 00:44:11 UTC
f7b1f67 Daniel Himmelstein 18 March 2016, 00:08:04 UTC Freeze excel header rows 18 March 2016, 00:08:04 UTC
9e29b0c Daniel Himmelstein 17 March 2016, 18:30:59 UTC Improve DWPC query Change `paths` to `path`. Singular better expresses the query plan. 17 March 2016, 18:31:31 UTC
e8bcd98 Daniel Himmelstein 17 March 2016, 18:24:53 UTC Activate `unique_nodes` by default Simplify the `format_expanded_clause` query to use not equals (`<>`). 17 March 2016, 18:24:53 UTC
d16f26b Daniel Himmelstein 11 March 2016, 23:46:44 UTC Merge branch 'master' of github.com:dhimmel/hetio 11 March 2016, 23:46:44 UTC
d524498 Daniel Himmelstein 11 March 2016, 23:46:34 UTC Sort metanodes and metaeges in writable_from_metagraph 11 March 2016, 23:46:34 UTC
b53848c Daniel Himmelstein 08 March 2016, 15:20:07 UTC Enable ftp:// and ftps:// url support 08 March 2016, 15:20:07 UTC
ac3d331 Daniel Himmelstein 29 February 2016, 00:49:37 UTC Bug fixes 29 February 2016, 00:49:37 UTC
cdf7dfc Daniel Himmelstein 29 February 2016, 00:06:43 UTC Add metanode to degree_df functionality 29 February 2016, 00:06:43 UTC
fe66a5b Daniel Himmelstein 28 February 2016, 22:40:05 UTC Add join index hint Adds `USING JOIN ON` index hint in `construct_dwpc_query()` when `using=True`. Previously, this hint was not included due to a bug in neo4j 2.3.1. See https://github.com/neo4j/neo4j/pull/5038#issuecomment-162098241 28 February 2016, 22:40:05 UTC
a6c8a28 Daniel Himmelstein 22 February 2016, 21:45:13 UTC Standardize metaedge abbreviations Switch from arranging by text to non-inversion when standardizing metaedge abbreviations. Remove direction indicators (inequality symbols), in standardized abbreviations. 22 February 2016, 21:45:13 UTC
9681f11 Daniel Himmelstein 22 February 2016, 21:09:04 UTC Exclude inverted edges The user will almost always want to see each metaedge once. Fixes a bug where undirected edges with the same source and target metanode had incorrect counts. 22 February 2016, 21:09:04 UTC
5e3647a Daniel Himmelstein 18 February 2016, 01:14:22 UTC Add bzip2 read/write support Refactor file handling. 18 February 2016, 01:14:22 UTC
9370d71 Daniel Himmelstein 17 February 2016, 02:35:19 UTC Change statistics reporting Switch from printing to a mix of logging and returning stats. Fixed a index bug in stat reporting. 17 February 2016, 02:35:19 UTC
9facc4b Daniel Himmelstein 06 January 2016, 16:48:18 UTC Neo4j XSwap bug fixes Fix swap so: ``` u-->v y v ^ ^ becomes | | x-->y u x ``` Remove property transfer which was causing a relationship not found bug. Use cypher `id` function rather than attribute. Switch incorrect slashes to backslashes. Fix random index selection. 06 January 2016, 17:00:44 UTC
f8d23c3 Daniel Himmelstein 29 December 2015, 03:07:23 UTC Add untested Xswap permutation 29 December 2015, 03:07:23 UTC
1aa1964 Daniel Himmelstein 19 December 2015, 23:30:19 UTC Add permutation module To perform randomized edge swaps on the hetnet. 19 December 2015, 23:30:19 UTC
de3b607 Daniel Himmelstein 14 December 2015, 01:19:12 UTC Make all Cypher functions lowercase 14 December 2015, 01:19:12 UTC
0683f5f Daniel Himmelstein 14 December 2015, 00:48:58 UTC Label-aware expanded node uniqueness constraint Add an method for specifying node uniqueness in a path that leverages known node labels. See https://doi.org/10.15363/thinklab.d134#2 14 December 2015, 00:48:58 UTC
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