Torchcell

Feature

* FEAT: bump feat to auto correct pypi ([`db9bd13`](https://github.com/Mjvolk3/torchcell/commit/db9bd1392b197792c61cdd25bffd7bdc41e141a2))

Fix

* BLD: refactor datasets and adapaters ([`6dad8d8`](https://github.com/Mjvolk3/torchcell/commit/6dad8d8ef692f26bd1fb85c1ec47c089f7820057))

Unknown

* next bump software version, bump image version ([`902269f`](https://github.com/Mjvolk3/torchcell/commit/902269f32aa85a6b109e254f203ab26df12bc52b))

* kuzmin dataset refactored ([`d1058a0`](https://github.com/Mjvolk3/torchcell/commit/d1058a0c50c1b8cad6cf40957741abda4ef4a35f))

* refactor of dataset ([`71a89c5`](https://github.com/Mjvolk3/torchcell/commit/71a89c5a6f49e1feb590d8a5fd2dafb62e9c84df))

* DmfCostanzoAdapter working. Had to add: transform item function, and make sure that the dataset is model.dumping ([`f6257dd`](https://github.com/Mjvolk3/torchcell/commit/f6257dd7a6883937407c0312c3137734b96290f2))

* deleted scratch note ([`8b895ea`](https://github.com/Mjvolk3/torchcell/commit/8b895ea98a9d450b7a3391408f34bdd867e6cf02))

* costanzo adapter working ([`bcfa141`](https://github.com/Mjvolk3/torchcell/commit/bcfa141dfeec9cf99761a549cc4a8821bea86162))

* workspace open random note script ([`ceeb187`](https://github.com/Mjvolk3/torchcell/commit/ceeb1873f1b70235a9f5b54fbeffa6475bbbd9be))

* workspace update ([`fbf3ac9`](https://github.com/Mjvolk3/torchcell/commit/fbf3ac94a59f8f05bee626aa9e609a381df5297f))

* note update ([`4b25bbd`](https://github.com/Mjvolk3/torchcell/commit/4b25bbd363103f8fda35e4b5b58f02deb07aa5ea))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4f56d85`](https://github.com/Mjvolk3/torchcell/commit/4f56d85cd69ae7bd3f924a5384a55590de28c063))

* Custom Data Loader threading, working SmfCostanzo2016 ([`ebebede`](https://github.com/Mjvolk3/torchcell/commit/ebebede480982408213af68b5428b581a6f2b8e0))

* notes update ([`c0dbf52`](https://github.com/Mjvolk3/torchcell/commit/c0dbf526d15bfe0dbf4b7abb1b8a52029a340fa1))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`36840fe`](https://github.com/Mjvolk3/torchcell/commit/36840fe5a6d5548445056692df71cdbedf03b415))

* update config for more mem on interactive cpu ([`0fdc64b`](https://github.com/Mjvolk3/torchcell/commit/0fdc64b6011086cfe27e96f69f876076be50ee94))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9ac3112`](https://github.com/Mjvolk3/torchcell/commit/9ac31121376c4bb545facf7676487781afb3077f))

* notes update ([`1b3a895`](https://github.com/Mjvolk3/torchcell/commit/1b3a895fcc57710dd44572c296cc1a871e19436d))

* update schema config ([`0c0f6d2`](https://github.com/Mjvolk3/torchcell/commit/0c0f6d22ac1af7e8dfc2b8daf6af3f11c9269800))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9a3d0b4`](https://github.com/Mjvolk3/torchcell/commit/9a3d0b45a78f43b14f91b43a42ef6d5ce33ed82c))

* updated build ([`7ca15ba`](https://github.com/Mjvolk3/torchcell/commit/7ca15ba2ca1423d7c17e0855158410c024d608dd))

* checking node write speed on delta ([`92fa143`](https://github.com/Mjvolk3/torchcell/commit/92fa143dfbe76a995c2b9fdef201e24267135b86))

* tasks update ([`e480079`](https://github.com/Mjvolk3/torchcell/commit/e48007905e6462dc319c55e1e2d796c96ce3df46))

* SmfCostanzo2016 get_nodes refactor with base class. All three optimizations implemented. ([`e1b2baa`](https://github.com/Mjvolk3/torchcell/commit/e1b2baa61be50d8da7861012a7ad6a68e0f5a957))

* custom loader delta test ([`741f862`](https://github.com/Mjvolk3/torchcell/commit/741f862db40f5374653b5dc7ba9dbbdee8353d8f))

* remove error... needs to run delta iter test again ([`e8e33a1`](https://github.com/Mjvolk3/torchcell/commit/e8e33a12340c5a399faa8e96b86900ebbbc4ceaf))

* trying to iterative over, didn&39;t before, dcell test, no write ([`b257139`](https://github.com/Mjvolk3/torchcell/commit/b25713959f4516b7fbe27c467534b8d22f7490e2))

* iteration of all fitness delta test ([`3b4f266`](https://github.com/Mjvolk3/torchcell/commit/3b4f26632193a37d8000095942c39dc57ffdc8c2))

* no writing of nodes, just iteration for delta test ([`98911ea`](https://github.com/Mjvolk3/torchcell/commit/98911ea81fdb231b5f77916be9755bb9b93b3402))

* print out num workers ([`efe7417`](https://github.com/Mjvolk3/torchcell/commit/efe7417e393792a0a67663d18a55c0a3a85064d3))

* only smf for delta speed test ([`8440797`](https://github.com/Mjvolk3/torchcell/commit/844079710918fe3dff7c116fe961935d6390239c))

* update remote build ([`c0d0724`](https://github.com/Mjvolk3/torchcell/commit/c0d07240d2e95e6018a8a2d70e05aec9afbcfa94))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7cbb6bf`](https://github.com/Mjvolk3/torchcell/commit/7cbb6bf943820dbb861a7fb90a0cef3f86dd0278))

* workers for slurm ([`f6628ab`](https://github.com/Mjvolk3/torchcell/commit/f6628abbace436543b8bf7b64023c307aedf6e10))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`c487a88`](https://github.com/Mjvolk3/torchcell/commit/c487a88d4bb52a331973744212b303616eefb6e4))

* linux amd troubleshooting and simplification via bash script ([`2775c66`](https://github.com/Mjvolk3/torchcell/commit/2775c66f1923cb3991480f8065e12e9e30ff09c7))

* all small delta test ([`5ca61e7`](https://github.com/Mjvolk3/torchcell/commit/5ca61e715f3c96ffedecdac92bdaec61da2ed973))

* task note update and frontmatter ([`dbfd86e`](https://github.com/Mjvolk3/torchcell/commit/dbfd86e1096fd02f8b7e84967dd40496b5aea382))

* switching logging to printing so we can try to suppress the prints in getting bash script in apptainer sif ([`d9fe49c`](https://github.com/Mjvolk3/torchcell/commit/d9fe49c9401d79dd3f2ae5c5b9787cce9d0118b6))

* rever to small with only SmfKuzmin ([`ebc79d8`](https://github.com/Mjvolk3/torchcell/commit/ebc79d8d9aff72d62eea7873c1252ef0ed6d0387))

* local m1 small build complete. ([`9469ff4`](https://github.com/Mjvolk3/torchcell/commit/9469ff4462c4a4dc7b67a2183a8c320a2a7046fb))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d0e6fc6`](https://github.com/Mjvolk3/torchcell/commit/d0e6fc60fa8bd5847d5b7525e7d29d042699ac79))

* TmfKuzmin2018Adapter test ([`a504d2c`](https://github.com/Mjvolk3/torchcell/commit/a504d2cb173dbc5be9c9456db9516073c88b4578))

* build slurm script update ([`6f9857d`](https://github.com/Mjvolk3/torchcell/commit/6f9857d5c4bedb5bb852be4a9f2c1aa0b29a3c3e))

* fixed interactive mode, DmfKuzmin2018Adapter test ([`e16fe48`](https://github.com/Mjvolk3/torchcell/commit/e16fe48389373f28039050606eba11a678569376))

* comments update ([`d30d335`](https://github.com/Mjvolk3/torchcell/commit/d30d33593e068449baa3a4922ffde48046e5dac4))

* SmfKuzmin2018Adapter test import ([`d22fc50`](https://github.com/Mjvolk3/torchcell/commit/d22fc50077b9706be8794f72aaaea8461aca40a1))

* DmfCostanzo2016Adapter_1e5 test import ([`5f3f59e`](https://github.com/Mjvolk3/torchcell/commit/5f3f59e952a631777d478a777e49b37fea363d05))

* SmfCostanzo2016 test ([`b090706`](https://github.com/Mjvolk3/torchcell/commit/b090706971fbed6a64eec7285205608782e7734a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`57bb9e3`](https://github.com/Mjvolk3/torchcell/commit/57bb9e30b68f849b3f3b26557efbefeca57d8140))

* close_lmdb before parallelization every time after data is accessed in class methods ([`872daea`](https://github.com/Mjvolk3/torchcell/commit/872daea0d78b950adafac1690b745c5a29048f10))

Fix

* MAINT: scipy parser ([`5475aa1`](https://github.com/Mjvolk3/torchcell/commit/5475aa138e6626e5eb7cf5991cc8e4663a3daa88))

Unknown

* drawings and build ([`0c07330`](https://github.com/Mjvolk3/torchcell/commit/0c0733044eabc1dfc279db2ca71e33ddc4bf5ced))

* update builds ([`333f38c`](https://github.com/Mjvolk3/torchcell/commit/333f38c5c2ea1b622d8b7992f5723e8e5b774859))

* update output dir again according the .env in local v docker, updated .env ([`72ad28c`](https://github.com/Mjvolk3/torchcell/commit/72ad28cfe5b8daad861506d356e45217df3588c9))

* update output dir ([`913cee6`](https://github.com/Mjvolk3/torchcell/commit/913cee6111c5861d6cae45d2ff1eb1eca0192d50))

* update graph to working smf kuzmin ([`0781e27`](https://github.com/Mjvolk3/torchcell/commit/0781e27c3f3e47359e37082a556857927eb03977))

* perfecting the config ([`8b3b0b0`](https://github.com/Mjvolk3/torchcell/commit/8b3b0b0f12480919fcddc0a612caf6a9c30ad302))

* docker local first small build bulk import ([`80ea50d`](https://github.com/Mjvolk3/torchcell/commit/80ea50dd95d3d508c7a1eb186711f92bcdee01ff))

* builds for delta matching local database pattern ([`2dcc4d4`](https://github.com/Mjvolk3/torchcell/commit/2dcc4d49fb10cd6a84ae0c5d0894511ee5a1d248))

* note typos ([`3d30103`](https://github.com/Mjvolk3/torchcell/commit/3d301035d7fe5cba26e9bb679ade187cb63cd52e))

* versioning SOP note ([`a9e741c`](https://github.com/Mjvolk3/torchcell/commit/a9e741c2ada7bbd7ef070bc7418cb72648f8484d))

Unknown

* fix: bumpversion example, lots of db local-packages ([`ee61890`](https://github.com/Mjvolk3/torchcell/commit/ee61890877828d904ab0871e44c19a5589551de7))

* removed python publish since cannot condition on semantic release ([`78683c8`](https://github.com/Mjvolk3/torchcell/commit/78683c836d892f49c2d223f23922be5f924b7a04))

Unknown

* fix: tc_publish_pypi code action, partial automation ([`097b44f`](https://github.com/Mjvolk3/torchcell/commit/097b44f95f514e4e9a67ca73bd6373e2438ed8fe))

Unknown

* fix: publishing scripts pypi ([`a367116`](https://github.com/Mjvolk3/torchcell/commit/a3671166939e117e3ce353310b29268f89548bb9))