https://github.com/dhimmel/hetio

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74ffd2c retire python 3.4, add python 3.8 (#48) merges https://github.com/hetio/hetnetpy/pull/48 python 3.4 began failing builds https://travis-ci.com/hetio/hetnetpy/jobs/265318129#L209 3.4 past official end of life 10 December 2019, 16:09:23 UTC
02b3131 Travis CI: use API token for PyPI authentication 11 September 2019, 15:30:26 UTC
4edea3e neo4j.construct_pdp_query: aggregate_columns option to return PC & DWPC (#47) Merges https://github.com/hetio/hetnetpy/pull/47 Refs https://github.com/greenelab/hetmech-backend/issues/64 30 July 2019, 19:12:39 UTC
43294c3 Style: blacken .py files, CI & pre-commit-hook checks (#46) Merges https://github.com/hetio/hetnetpy/pull/46 References: https://github.com/python/black https://black.readthedocs.io/en/stable/version_control_integration.html https://www.mattlayman.com/blog/2018/python-code-black/ https://hynek.me/articles/conditional-python-dependencies/ https://unix.stackexchange.com/a/22728/294987 https://unix.stackexchange.com/a/48806/294987 12 July 2019, 17:23:26 UTC
7ebf720 Update badges to include logos https://shields.io/category/build https://simpleicons.org/ [skip ci] 12 July 2019, 15:20:43 UTC
b9a2836 CI for Windows using AppVeyor (#45) Merges https://github.com/hetio/hetnetpy/pull/45 Add .appveyor.yml configuration and badge. Reorder README badges Use setuptools.find_packages hetio symlink directory does not seem to work on Windows: https://ci.appveyor.com/project/hetio/hetnetpy/builds/25938369/job/h4x1hf4b33xuhpy0#L25 ``` error: supposed package directory 'hetio' exists, but is not a directory ``` Disable import hetio test for Windows Cache pip installs: https://www.appveyor.com/docs/build-cache/ https://gitlab.freedesktop.org/mesa/mesa/commit/8550be7a2fd151e050932c9fc1349b93ab1b9992 12 July 2019, 15:06:22 UTC
d678eb7 Housekeeping: travis and setup updates (#43) Merges https://github.com/hetio/hetnetpy/pull/43 Travis updates: - cache pip installs - remove GitHub Releases upload Has not worked since v0.2.6 (since hetio organization relocation) https://github.com/hetio/hetnetpy/releases/tag/v0.2.6 These files are available on PyPI. Change import of neo4j: neo4j.v1 package is deprecated hetio/hetnetpy/test/neo4j_test.py:2: DeprecationWarning: The 'neo4j.v1' package is deprecated, import from 'neo4j' instead 11 July 2019, 16:14:38 UTC
d88f81a Rename codebase to use hetnetpy from hetio Merges https://github.com/hetio/hetnetpy/pull/42 Closes https://github.com/hetio/hetnetpy/issues/40 `pip install hetnetpy` now installs two packages: hetnetpy and hetio. `import hetio` will trigger a warning. The source code uses a symbolic link. Behavior on windows unknown. 10 July 2019, 23:39:03 UTC
83e58bc release v0.2.11 to warn about future rename to hetnetpy Merges https://github.com/hetio/hetio/pull/41 Refs https://github.com/hetio/hetio/issues/40 10 July 2019, 21:56:47 UTC
f8aab19 Update .gitignore 10 July 2019, 18:55:33 UTC
84f1665 Prepare v0.2.10 release 02 May 2019, 18:26:47 UTC
42c9c90 is_symmetric method for metapaths Merges https://github.com/hetio/hetio/pull/39 Closes https://github.com/hetio/hetio/issues/38 Create only a single object for a symmetric metapath and its inverse. 02 May 2019, 01:53:44 UTC
6afb591 Migrate neo4j nomenclature to hetnet module Merges https://github.com/hetio/hetio/pull/37 * Migrate neo4j nomenclature to hetnet module * neo4j terminology lookup in get_metanode / get_metaedge 22 April 2019, 20:25:13 UTC
5a77399 hetio.neo4j.create_path_return_clause: id_lists option Merge https://github.com/hetio/hetio/pull/36 Refs https://github.com/greenelab/hetmech-backend/issues/31#issuecomment-484602973 Also switchs to neo4j cypher list comprehension 19 April 2019, 19:48:26 UTC
0568e3f Lazy import third-party deps in hetio.neo4j Merges https://github.com/hetio/hetio/pull/35 Prevents ModuleNotFoundError when the functions called may not actually need the missing package. 19 April 2019, 17:50:48 UTC
7c179b7 Changed PERCENT_OF_DWPC to percent_of_DWPC Merges https://github.com/hetio/hetio/pull/34 28 January 2019, 21:40:54 UTC
9a2a218 neo4j.construct_pdp_query: optimize, refactor, test Merges https://github.com/hetio/hetio/pull/33 * Refactor code shared between construct_pdp_query and construct_dwpc_query into a function. * Optimized construct_pdp_query to run faster, using query from https://stackoverflow.com/a/54245650/4651668 with additional removal of unnecessary UNWIND and WITH statements * Added the return_property parameter to create_path_return_clause to allow node identifiers other than name. * Replaced the create_path_return_clause function with two better formatted tests. Use read_metagraph for obtaining metagraphs in neo4j_test. 25 January 2019, 19:54:16 UTC
7280c58 Separate py2neo import to fix httpstream ImportError Merges https://github.com/hetio/hetio/pull/32 Closes https://github.com/hetio/hetio/issues/31 21 January 2019, 19:25:27 UTC
956f0de Add construct_pdp_query to build cypher queries for PDP Merges https://github.com/hetio/hetio/pull/30 * Added the function construct_pdp_query to build cypher queries that calculate the path degree product * Added tests for construct_pdp_query and construct_dwpc_query * Updated the test dependencies in setup.py * Modified the neo4j tests to only read a subsection of the graph so they would run faster and with less memory (and as a result stop breaking travis) 10 January 2019, 21:03:39 UTC
e793abf Updated neo4j.py with fix from zietzm's review 10 January 2019, 18:52:31 UTC
5bdb20a Modified the neo4j tests to only read a subsection of the graph so they would run faster and with less memory (and as a result stop breaking travis 09 January 2019, 22:04:10 UTC
3845f1a Put the rest of the neo4j.py dependencies in the test dependencies for setup.py 09 January 2019, 18:58:07 UTC
df9978f Added neo4j to the test dependencies 09 January 2019, 17:25:25 UTC
7afa1e3 Added tests for construct_pdp_query and construct_dwpc_query 09 January 2019, 17:02:56 UTC
55e2d72 Added the function construct_pdp_query to build cypher queries that calculate the path degree product 08 January 2019, 21:05:54 UTC
52a41c7 permute_pair_list: default to inplace=False Closes https://github.com/hetio/hetio/issues/28 Adds test for permute_pair_list. Fixes unrelated filename typo. 05 December 2018, 18:52:51 UTC
1a1da50 Consistent metanode/metaedge/metapath .abbrev property Merges https://github.com/hetio/hetio/pull/27 Consistent metanode/metaedge/metapath .abbrev method Test metaedge/metapath.abbrev property 06 November 2018, 22:11:40 UTC
ae2d0bc Fix typo in permute.permute_pair_list docstring Merges https://github.com/hetio/hetio/pull/26 16 August 2018, 15:14:38 UTC
5e8ca21 Upgrade to v0.2.9 Merges https://github.com/hetio/hetio/pull/25 15 August 2018, 19:27:46 UTC
2fe1c30 Document hetio.permute functions Merges https://github.com/hetio/hetio/pull/24 15 August 2018, 19:18:06 UTC
958b0ae Relocate repo from dhimmel/hetio to hetio/hetio Merges https://github.com/hetio/hetio/pull/23 09 August 2018, 19:37:41 UTC
4657926 Travis config: fix indent 08 August 2018, 14:44:41 UTC
f5dd406 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 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 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 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 Convenience function: metagraph.get_metapath Squash merges https://github.com/dhimmel/hetio/pull/19 18 May 2018, 21:59:25 UTC
6e7ee73 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 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 setup.py: PyPI now supports markdown long_description 24 April 2018, 20:10:31 UTC
aa5d12e 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 Simplify .gitignore 05 April 2018, 20:50:14 UTC
21c6443 readwrite: support pathlike objects 05 April 2018, 20:45:59 UTC
f60f95d DOC: abbreviation regex pattern comment 04 April 2018, 21:26:28 UTC
98564d6 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 Upgrade to v0.2.8 27 March 2018, 14:36:44 UTC
7f33036 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 Rename fxn to sparsify_or_densify & tests 27 March 2018, 14:26:01 UTC
c21189f Refine matrix code & incoporate into hetio 27 March 2018, 14:26:01 UTC
fc7f108 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 Upgrade to v0.2.7 15 February 2018, 15:25:07 UTC
9f66bd4 Update README with eLife publication 22 September 2017, 19:14:38 UTC
30c6dbb Create Hetionet v1.0 subgraph with all metanodes 01 June 2017, 19:36:24 UTC
62c4dd1 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 Test traversal on CbGpPWpGaD subgraph 31 May 2017, 15:53:48 UTC
e72e513 Improve kind_to_abbrev subsetting in get_subgraph 31 May 2017, 15:53:03 UTC
dcb04eb get_subgraph to subset hetnets 30 May 2017, 18:50:05 UTC
86c1114 Specify python_requires in setup.py 20 April 2017, 15:55:41 UTC
56f6262 Upgrade to v0.2.6 04 April 2017, 20:08:44 UTC
f7b6ccb TST: test GeTlD metapath in gene-disease example 04 April 2017, 20:06:48 UTC
2562850 Style: flake8 abbreviation.py 01 April 2017, 20:34:07 UTC
13436b2 Style: flake8 pathtools.py 01 April 2017, 20:23:40 UTC
a7aaded Fix node __repr__ in notebook 01 April 2017, 19:33:10 UTC
9dc747b Doc & Style: flake8 and docstrings 01 April 2017, 18:17:08 UTC
4591708 Add PC / DWPC test 01 April 2017, 18:03:04 UTC
a0e904a BUG: add missing edges, fix path name In disease-gene-example-graph test 01 April 2017, 17:59:07 UTC
1045b84 Style: flake8 graph_test.py 01 April 2017, 17:35:19 UTC
7eedc98 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 ENH: support source/target node in add_edge 01 April 2017, 17:03:38 UTC
0b3ccb7 Upgrade to v0.2.5 28 March 2017, 14:43:07 UTC
f284014 Fix README command for __version__ 28 March 2017, 14:42:46 UTC
558e379 Travis: github releases use @hetio-release-bot 28 March 2017, 13:51:44 UTC
488d603 Add hetio.__version__ support See https://packaging.python.org/single_source_version/ 18 March 2017, 21:06:18 UTC
525837a Upgrade to v0.2.4 17 March 2017, 21:15:42 UTC
a7c2755 Style: satisfy flake8 in hetio.readwrite 17 March 2017, 21:02:10 UTC
421860c Remove yaml readwrite support 17 March 2017, 20:59:56 UTC
f21a73b Remove requests dependency. Test metagraph reading Remove examples since metagraphs move to test/data. 17 March 2017, 19:56:58 UTC
432f14b Reformat setup.py. Configure extras_require 16 March 2017, 17:45:39 UTC
3e236ef Improve hetio.hetnet style 16 March 2017, 17:28:42 UTC
4f5bfa5 Add release instructions 03 March 2017, 01:57:06 UTC
1e00ce4 Upgrade to v0.2.3 03 March 2017, 01:03:50 UTC
24b2036 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 Upgrade to v0.2.2 02 March 2017, 23:57:34 UTC
cbfd4c3 Travis PyPI deploy: add wheel 02 March 2017, 23:46:45 UTC
2587193 Limit deployment to Python 3.6 job only 02 March 2017, 23:34:01 UTC
a34946f Remove register.py, switching to Travis deploy 02 March 2017, 23:29:01 UTC
8858d78 Travis CI: deploy to PyPI 02 March 2017, 23:23:09 UTC
0b7baab Travis CI: deploy to GitHub Releases 02 March 2017, 23:23:09 UTC
8f74660 Use pandoc to generate README.rst Closes https://github.com/dhimmel/hetio/issues/7 02 March 2017, 22:47:41 UTC
91562f7 Expand setup.py lists 02 March 2017, 22:10:21 UTC
d026d13 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 Minor cleaning of neo4j.py 02 March 2017, 21:36:53 UTC
7fe01f1 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 Disable failing pytest feature in travis py34 16 February 2017, 00:28:25 UTC
d32ba2a Add support for bidirectional self-loop edges Do not allow the adding of duplicate edges. 16 February 2017, 00:23:24 UTC
8531e2b Improve tests 15 February 2017, 23:35:03 UTC
7472d90 Make abbreviation tests pytest discoverable 15 February 2017, 23:06:00 UTC
0799fe3 Add Travis CI 15 February 2017, 22:35:59 UTC
903a4c8 Count nodes and edges in graph 15 February 2017, 22:18:32 UTC
69aea62 Fix tests with updated import path 15 February 2017, 22:17:16 UTC
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