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Jnmpi lammps nodes patch 0.1.0 #91

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merged 95 commits into from
Nov 28, 2023
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518f545
Rename parameter and pull it up to parent class
liamhuber Nov 3, 2023
589db19
Type check value assignment
liamhuber Nov 3, 2023
65e3b3a
Add type hint checks to the value receiver assignment
liamhuber Nov 3, 2023
80a91f6
Use convenience method
liamhuber Nov 3, 2023
e2b292e
Remove useless method
liamhuber Nov 3, 2023
6248f88
Avoid type hinting if it was done earlier
liamhuber Nov 3, 2023
8d7e372
No, just type check when its asked for
liamhuber Nov 3, 2023
29a330d
Add node level shortcut for (de)activating strict hinting
liamhuber Nov 3, 2023
9e0db4c
Add to docstring
liamhuber Nov 3, 2023
5dbf769
Let InputData just take DataIO docstring
liamhuber Nov 3, 2023
cd5bc2e
Add missing whitespace in error message
liamhuber Nov 4, 2023
301d164
Improve formatting for type error message
liamhuber Nov 4, 2023
5001914
Update Function docs
liamhuber Nov 4, 2023
b5604af
Update Channels docs
liamhuber Nov 4, 2023
df6934c
Update example notebook
liamhuber Nov 4, 2023
a52d8c8
Format black
pyiron-runner Nov 4, 2023
a83be99
Merge pull request #66 from pyiron/value_validation
liamhuber Nov 4, 2023
3beb615
Bump matplotlib from 3.8.0 to 3.8.1
dependabot[bot] Nov 6, 2023
ec08b2d
[dependabot skip] Update environment
pyiron-runner Nov 6, 2023
354ad9e
[dependabot skip] Update env file
pyiron-runner Nov 6, 2023
3732bf8
Merge pull request #69 from pyiron/dependabot/pip/matplotlib-3.8.1
liamhuber Nov 6, 2023
d0f7704
Update channel docs and test to them
liamhuber Nov 6, 2023
4f76dc5
Never allow input data updates while the parent node is running
liamhuber Nov 6, 2023
a9381c8
Update Node docs and make tests for the base class
liamhuber Nov 6, 2023
f138999
Draft module-level overview for API docs/use in readme
liamhuber Nov 6, 2023
70f0d98
Test single point of import
liamhuber Nov 6, 2023
35b5c0e
:bug: fix the expected error to be raised
liamhuber Nov 6, 2023
300ad1c
Update IO docstring
liamhuber Nov 6, 2023
5f567f0
Update Function docstring
liamhuber Nov 6, 2023
7fd250e
Update function tests
liamhuber Nov 6, 2023
37c2262
Test the call aliases
liamhuber Nov 6, 2023
dbddd14
Update Composite docs
liamhuber Nov 10, 2023
7739aeb
Improve working directory test
liamhuber Nov 10, 2023
aa01945
Update composite promises
liamhuber Nov 10, 2023
27ce1d5
:bug: actually iterate over child nodes
liamhuber Nov 10, 2023
fff90cf
Pull up the IO rebuild check after node replacement
liamhuber Nov 10, 2023
a02adee
Test the promises made in Composite directly
liamhuber Nov 10, 2023
bcce14d
Make Macro's graph_creator available as a class method
liamhuber Nov 10, 2023
7d9238e
Use setUp
liamhuber Nov 10, 2023
6e88ef3
Define and test Macro promises
liamhuber Nov 10, 2023
8a31793
Make and test Workflow promises
liamhuber Nov 10, 2023
53557cf
:bug: handle bidict None duplication
liamhuber Nov 11, 2023
2eda950
:bug: check for instance type
liamhuber Nov 11, 2023
811fb79
Apply de-duplication of None values to both I and O
liamhuber Nov 11, 2023
6eab6ae
:bug: make sure the map is persistent
liamhuber Nov 11, 2023
0577034
Pull the bijectivity tests up to Composite
liamhuber Nov 11, 2023
2554682
Reformat Function as promises
liamhuber Nov 11, 2023
29a4b29
Finish parent promises
liamhuber Nov 11, 2023
414d1c5
Update node docs to the "promises" format
liamhuber Nov 11, 2023
8f2b40c
Reorder node tests to better match the order of the promises
liamhuber Nov 11, 2023
cb47ed2
Remove redundant topology tools
liamhuber Nov 11, 2023
d674887
Make method private
liamhuber Nov 11, 2023
ab2435a
Format black
pyiron-runner Nov 11, 2023
75881f7
Add a short sleep
liamhuber Nov 11, 2023
9a47ca9
Update example notebook
liamhuber Nov 11, 2023
724bce7
Rename and re-run the example notebook
liamhuber Nov 11, 2023
290a282
Add quickstart notebook
liamhuber Nov 11, 2023
2f2c79b
Add badges to readme
liamhuber Nov 11, 2023
fc6dcd0
Update overview
liamhuber Nov 11, 2023
3b65a35
Add tailing readme sections
liamhuber Nov 11, 2023
4538443
Update readme code example
liamhuber Nov 11, 2023
4ec4d72
Update the docs badge
liamhuber Nov 11, 2023
7b02bc0
Merge pull request #70 from pyiron/spec_and_test
liamhuber Nov 11, 2023
af12c58
Nodes for the `atomistics` package
jan-janssen Nov 15, 2023
99511e7
remove `output_labels` kwargs - switch to args
jan-janssen Nov 16, 2023
d28bd0b
Add Macro nodes
jan-janssen Nov 16, 2023
20d4658
Define an internal macro to reduce code duplication
jan-janssen Nov 16, 2023
27e35f1
black formatting
jan-janssen Nov 16, 2023
c248151
Add `nodes: list[Node]` attribute to the node packages
liamhuber Nov 16, 2023
dab4659
Format black
pyiron-runner Nov 19, 2023
82f1b4b
Merge pull request #79 from pyiron/make_py_files_node_packages
liamhuber Nov 19, 2023
3fb7c28
Make macros with a meta node
liamhuber Nov 19, 2023
dcd948b
Remove the old versions
liamhuber Nov 19, 2023
d392890
Format black
pyiron-runner Nov 20, 2023
1b8cf3c
Merge pull request #78 from pyiron/atomistics_library
jan-janssen Nov 20, 2023
45737b6
Merge pull request #80 from pyiron/refactor_macros
liamhuber Nov 20, 2023
fae107c
Handle actions itself in the dependabot updates
niklassiemer Nov 23, 2023
ee6c049
Bump matplotlib from 3.8.1 to 3.8.2
dependabot[bot] Nov 23, 2023
39d4a84
[dependabot skip] Update environment
pyiron-runner Nov 23, 2023
28bb4dd
[dependabot skip] Update env file
pyiron-runner Nov 23, 2023
ccd571f
Merge pull request #82 from pyiron/dependabot/pip/matplotlib-3.8.2
liamhuber Nov 23, 2023
1a713b2
Bump pyiron-base from 0.6.8 to 0.6.9
dependabot[bot] Nov 23, 2023
f45285d
[dependabot skip] Update environment
pyiron-runner Nov 23, 2023
acd81cd
[dependabot skip] Update env file
pyiron-runner Nov 23, 2023
803a915
Merge pull request #83 from pyiron/dependabot/pip/pyiron-base-0.6.9
liamhuber Nov 23, 2023
f0ab225
Bump pyiron-atomistics from 0.3.5 to 0.3.7
dependabot[bot] Nov 23, 2023
bff74e3
Merge pull request #89 from pyiron/dependabot/pip/pyiron-atomistics-0…
jan-janssen Nov 23, 2023
56a7dfc
Merge pull request #88 from pyiron/dependabot_the_actions
liamhuber Nov 27, 2023
cb230e5
Merge branch 'main' into JNmpi_lammps_nodes_patch_0.1.0
liamhuber Nov 27, 2023
f2e15ac
Re-order notebooks env
liamhuber Nov 27, 2023
65f9f06
Remove binder maggma pin
liamhuber Nov 27, 2023
4d7ec2b
Conform to type hints
liamhuber Nov 27, 2023
4a29d7c
[dependabot skip] Update env file
pyiron-runner Nov 27, 2023
6c586fa
Add contrib to notebook deps
liamhuber Nov 27, 2023
361726f
[dependabot skip] Update env file
pyiron-runner Nov 27, 2023
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2 changes: 1 addition & 1 deletion .binder/environment.yml
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@ dependencies:
- bidict =0.22.1
- cloudpickle =3.0.0
- graphviz =8.1.0
- matplotlib =3.8.1
- matplotlib =3.8.2
- pyiron_base =0.6.8
- python-graphviz =0.20.1
- toposort =1.10
2 changes: 1 addition & 1 deletion docs/environment.yml
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@ dependencies:
- bidict =0.22.1
- cloudpickle =3.0.0
- graphviz =8.1.0
- matplotlib =3.8.1
- matplotlib =3.8.2
- pyiron_base =0.6.8
- python-graphviz =0.20.1
- toposort =1.10