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[Python 3.9] Improve isodesmic and add element balance constraints #2695

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merged 41 commits into from
Aug 5, 2024
Merged

[Python 3.9] Improve isodesmic and add element balance constraints #2695

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ca0091a
Update year in license
hwpang Jan 24, 2024
bd60215
imports sorting by formatter
hwpang Jan 24, 2024
d90e4fb
Add improvements by @amarkpayne
hwpang Jan 25, 2024
b78765f
Add constraints for element balance
hwpang Jan 24, 2024
1b052aa
Add pyutilib to catch ApplicationError
hwpang Jan 25, 2024
a929f2c
Formatting by formatter
hwpang Jan 25, 2024
57faf2f
Catch TypeError
hwpang Jan 25, 2024
6938a88
WIP
hwpang Jan 30, 2024
bd7f2b5
Modify based on review comment
hwpang Jun 11, 2024
bbc0030
Better way to initialize empty list
hwpang Jun 11, 2024
7fa4cf1
Improve code readability to get enumerated constraints
hwpang Jun 11, 2024
b28281d
Constraint cation/anion/neutral target to cation/anion/neutral refere…
hwpang Jun 11, 2024
3544b2f
Add warning for easy debugging
hwpang Jun 11, 2024
24bf4e5
Switch to use scipy
hwpang Jun 11, 2024
59e0cf1
Remove unused imports and correct obj fnc
hwpang Jun 11, 2024
fd96df6
Remove unused package, add version constraint to scipy
hwpang Jun 11, 2024
e75c15e
Remove options of solver
hwpang Jun 11, 2024
46e930f
Add comment to make test more readable
hwpang Jun 11, 2024
a61e34b
Use keyword variable
hwpang Jun 11, 2024
05a7d49
Add comment
hwpang Jun 11, 2024
e3cc59e
Add comment to test
hwpang Jun 11, 2024
bb44414
remove lpsolve55 from environments, tests, functions, docstrings, & docs
JacksonBurns Jul 24, 2024
d47a1f5
convert helper function args to kwargs for partial to work, hide func…
JacksonBurns Jul 24, 2024
54efa64
re-try running M1 macs on native hardware rather than x86 emulation
JacksonBurns Jul 24, 2024
12f2968
ugh, typo
JacksonBurns Jul 24, 2024
5407567
pass constraints as a tuple
JacksonBurns Jul 25, 2024
baf260a
fix return type for clar call
JacksonBurns Jul 25, 2024
db6e632
update return types in cython header
JacksonBurns Jul 25, 2024
91d74cd
yet more incorrect return types
JacksonBurns Jul 25, 2024
fb19d02
use python warnings module instead of removed numpy warnings passthrough
JacksonBurns Jul 25, 2024
f30b04a
fix incorrect use of `getattr`
JacksonBurns Jul 25, 2024
ff4ef4e
add back the cclib version restriction
JacksonBurns Jul 25, 2024
28d2fbf
allow empty return to be properly excepted
JacksonBurns Jul 25, 2024
be69fb2
fix usage of `n` for iteration
JacksonBurns Jul 25, 2024
5e7b266
make dict_keys -> str conversion explicit so it will run
JacksonBurns Jul 25, 2024
551926d
re-limit the version of cantera to undo the API breaks
JacksonBurns Jul 25, 2024
c1d6902
incorrect placement of parens
JacksonBurns Jul 25, 2024
10e79c2
make tuple cast more explicit
JacksonBurns Jul 26, 2024
46b9c92
explicit cast of set to str
JacksonBurns Aug 5, 2024
9092cd5
remove disused pyomo components
JacksonBurns Aug 5, 2024
4f8f268
fix usage of warning
JacksonBurns Aug 5, 2024
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2 changes: 0 additions & 2 deletions .conda/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@ requirements:
- {{ compiler('c') }} # [unix]
host:
- cython >=0.25.2
- lpsolve55
- numpy
- openbabel >=3
- pydas >=1.0.2
Expand All @@ -39,7 +38,6 @@ requirements:
- h5py
- jinja2
- jupyter
- lpsolve55
- markupsafe
- matplotlib >=1.5
- mopac
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10 changes: 0 additions & 10 deletions .github/workflows/CI.yml
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Expand Up @@ -81,16 +81,6 @@ jobs:
activate-environment: rmg_env
use-mamba: true

- name: Fix ARM Mac environment
if: matrix.os == 'macos-latest'
run: |
conda deactivate
conda env remove -n rmg_env
conda create -n rmg_env
conda activate rmg_env
conda config --env --set subdir osx-64
conda env update -f environment.yml

# list the environment for debugging purposes
- name: mamba info
run: |
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