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Tinybase: New Input/Output, Renamed Executors, Storage/Directory brokering by Project #949

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merged 47 commits into from
Feb 2, 2024
Merged

Tinybase: New Input/Output, Renamed Executors, Storage/Directory brokering by Project #949

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b858051
Rename Executors to Submitters to avoid name clash
pmrv Oct 6, 2023
7e177fe
REBASE: rename executor
pmrv Jan 2, 2024
c606d06
Move to dataclass based storage classes
pmrv Jan 2, 2024
48f611c
Add HasGroups to GenericStorage
pmrv Jan 4, 2024
6945fd3
Do not special case Storable in ProjectHDFioStorageAdapter
pmrv Jan 4, 2024
f575733
Add a GenericStorage directly using HDF5 files
pmrv Jan 4, 2024
b7fd2cd
Add two projects that use H5io directly; w/o pyiron_base adapters
pmrv Jan 4, 2024
1e32819
Add __delitem__ to storage interface
pmrv Jan 4, 2024
becd348
Update job examples
pmrv Jan 4, 2024
80f3f2f
Split project.py into a package
pmrv Jul 11, 2023
f8bc800
Add section to show new project types
pmrv Jan 4, 2024
2b5b12a
Update docstring
pmrv Jan 4, 2024
773861a
Add a small input class to capture computational parameters
pmrv Jan 5, 2024
0908fa7
Add method to projects to broker working directory
pmrv Jan 8, 2024
e5b1e05
Fix changing pympipool API
pmrv Jan 8, 2024
a55145e
Quick fix to avoid to_object natively stored things
pmrv Jan 8, 2024
3715fa4
Update notebook
pmrv Jan 8, 2024
485f2df
[dependabot skip] Update env file
pyiron-runner Jan 8, 2024
d0619fd
stick with h5io_browser==0.0.4 for dependency compat
pmrv Jan 8, 2024
c256bbb
[dependabot skip] Update env file
pyiron-runner Jan 8, 2024
f7d7f32
Merge branch 'main' into tinydata
pmrv Jan 8, 2024
e4ec4fd
Merge branch 'main' into tinydata
pmrv Jan 8, 2024
68dce7e
Bump versions again
pmrv Jan 9, 2024
1075ad0
[dependabot skip] Update env file
pyiron-runner Jan 9, 2024
dcd3193
Update setup.py
jan-janssen Jan 10, 2024
6ca8b87
Update setup.py
jan-janssen Jan 10, 2024
22b0505
Format black
pyiron-runner Jan 10, 2024
3a20c07
Bump h5io_browser again
pmrv Jan 15, 2024
b36777c
Update environment.yml
jan-janssen Jan 15, 2024
69cb1b0
[dependabot skip] Update env file
pyiron-runner Jan 15, 2024
f733f20
Update environment.yml
jan-janssen Jan 15, 2024
d75866a
[dependabot skip] Update env file
pyiron-runner Jan 15, 2024
7b6ab72
Sync setup dependencies
liamhuber Jan 15, 2024
ed8fb21
No mutable default
liamhuber Jan 15, 2024
c75eee7
Use available pympipool import
liamhuber Jan 15, 2024
4a65242
Black newline
liamhuber Jan 16, 2024
b9dced8
Purge pympipool from notebooks
liamhuber Jan 16, 2024
169a4e2
Merge pull request #962 from pyiron/lpatch_tinydata
liamhuber Jan 16, 2024
2608bab
Keep task context pure
pmrv Jan 26, 2024
bd04579
Update notebooks
pmrv Jan 26, 2024
84f33e0
Correctly use new output interface in shell/lammps tasks
pmrv Jan 26, 2024
2468982
[dependabot skip] Update env file
pyiron-runner Jan 26, 2024
39995a3
Update shell notebook
liamhuber Feb 2, 2024
4d1de6f
Format black
pyiron-runner Feb 2, 2024
90827cf
Try to navigate to the right place from papermill
liamhuber Feb 2, 2024
bdc5e33
Merge remote-tracking branch 'origin/tinydata_notebook_patch' into ti…
liamhuber Feb 2, 2024
53cfbe3
Merge pull request #978 from pyiron/tinydata_notebook_patch
liamhuber Feb 2, 2024
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3 changes: 2 additions & 1 deletion .binder/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ dependencies:
- coverage
- codacy-coverage
- matplotlib =3.8.2
- numpy =1.26.2
- numpy =1.26.3
- pyiron_base =0.6.20
- pyiron_atomistics =0.4.4
- pyparsing =3.1.1
Expand All @@ -20,6 +20,7 @@ dependencies:
- aws-sam-translator =1.77.0
- pympipool =0.7.9
- distributed =2023.12.1
- h5io_browser =0.0.5
- python >= 3.10
- lammps
- nglview >=3.0.8
Expand Down
3 changes: 2 additions & 1 deletion .ci_support/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ dependencies:
- coverage
- codacy-coverage
- matplotlib =3.8.2
- numpy =1.26.2
- numpy =1.26.3
- pyiron_base =0.6.20
- pyiron_atomistics =0.4.4
- pyparsing =3.1.1
Expand All @@ -20,3 +20,4 @@ dependencies:
- aws-sam-translator =1.77.0
- pympipool =0.7.9
- distributed =2023.12.1
- h5io_browser =0.0.5
3 changes: 2 additions & 1 deletion docs/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ dependencies:
- coverage
- codacy-coverage
- matplotlib =3.8.2
- numpy =1.26.2
- numpy =1.26.3
- pyiron_base =0.6.20
- pyiron_atomistics =0.4.4
- pyparsing =3.1.1
Expand All @@ -22,3 +22,4 @@ dependencies:
- aws-sam-translator =1.77.0
- pympipool =0.7.9
- distributed =2023.12.1
- h5io_browser =0.0.5
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